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Miura T, Kadoya SS, Miura Y, Takino H, Akiba M, Sano D, Masuda T. Pepper mild mottle virus intended for use as a process indicator for drinking water treatment: Present forms and quantitative relations to norovirus and rotavirus in surface water. Water Res 2024; 257:121713. [PMID: 38733963 DOI: 10.1016/j.watres.2024.121713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/19/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Pepper mild mottle virus (PMMoV) has been proposed as a potential indicator of human enteric viruses in environmental water and for viral removal during drinking water treatment. To investigate the occurrence and present forms of PMMoV and quantitative relations to norovirus GII and rotavirus A (RVA) in surface waters, 147 source water samples were collected from 21 drinking water treatment plants (DWTPs) in Japan between January 2018 and January 2021, and the concentrations of viruses in suspended and dissolved fractions were measured using real-time RT-PCR. PMMoV was detected in 81-100 % of samples in each sample month and observed concentrations ranged from 3.0 to 7.0 log10 copies/L. The concentrations of PMMoV were higher in dissolved fraction compared to suspended fractions, while different partitioning was observed for NoV GII depending on seasons. The concentrations of PMMoV were basically higher than those of norovirus GII (1.9-5.3 log10 copies/L) and RVA (1.9-6.6 log10 copies/L), while in 18 samples, RVA presented higher concentrations than PMMoV. Partial regions of VP7, VP4, and VP6 of the RVA in the 18 samples were amplified using nested PCR, and the genotypes were determined using an amplicon-based next-generation sequencing approach. We found that these source water samples included not only human RVA but also various animal RVA and high genetic diversity due to the existence of animal RVA was associated with a higher RVA concentration than PMMoV. Our findings suggest that PMMoV can be used as an indicator of norovirus GII and human RVA in drinking water sources and that the indicator performance should be evaluated by comparing to zoonotic viruses as well as human viruses.
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Affiliation(s)
- Takayuki Miura
- Department of Environmental Health, National Institute of Public Health, Wako, Japan.
| | - Syun-Suke Kadoya
- Department of Civil and Environmental Engineering, Tohoku University, Japan; Department of Urban Engineering, The University of Tokyo, Japan
| | - Yohei Miura
- Department of Civil and Environmental Engineering, Tohoku University, Japan
| | - Hiroyuki Takino
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Michihiro Akiba
- Department of Environmental Health, National Institute of Public Health, Wako, Japan
| | - Daisuke Sano
- Department of Civil and Environmental Engineering, Tohoku University, Japan
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Schwarz M, Gazdarica M, Froňková E, Svatoň M, Bronský J, Havlovicová M, Křepelová A, Macek M. Functional studies associate novel DUOX2 gene variants detected in heterozygosity to Crohn's disease. Mol Biol Rep 2024; 51:399. [PMID: 38456993 DOI: 10.1007/s11033-024-09317-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024]
Abstract
PURPOSE Crohn's disease is a chronic gastrointestinal inflammatory disease with possible extraintestinal symptoms. There are predisposing genetic factors and even monogenic variants of the disorder. One of the possible genetic factors are variants of the DUOX2 gene. The protein product of the DUOX2 gene is a dual oxidase enzyme producing H2O2 in the bowel. Reduced H2O2 levels impact mucosal homeostasis and contribute to the development of inflammatory bowel disease. Thus far, only 19 patients with IBD with the DUOX2 variants have been described. METHODS Here we present a case report of an adolescent female diagnosed at eleven years of age with IBD that was subsequently reclassified as Crohn's disease. She was treated with immunosuppressants and biological therapy but experienced additional complications. Her peripheral blood lymphocyte DNA was studied using massive parallel sequencing. Detected variants were functionally studied. RESULTS Whole exome sequencing found two novel DUOX2 gene variants: a de novo variant c.3646C>T; p.R1216W and a maternally inherited variant c.3391G>A; p.A1131T which were initially classified as variants of unknown significance. However, follow-up functional studies demonstrated that both DUOX2 variants led to impaired H2O2 generation, which led to their reclassification to the likely pathogenic class according to the ACMG.net. Therefore, we conclude that these variants are causative for the disease. CONCLUSIONS Identifying novel variants in patients with Crohn's disease and their families is important for precision medicine approaches and understanding of the pathogenesis of likely "monogenic" rare forms of inflammatory bowel disease.
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Affiliation(s)
- Martin Schwarz
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic.
- PRENET - Laboratoře Lékařské Genetiky s.r.o., Pardubice, Czech Republic.
| | - Matej Gazdarica
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Eva Froňková
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty, Childhood Leukaemia Investigation Prague, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Michael Svatoň
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty, Childhood Leukaemia Investigation Prague, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Jiří Bronský
- Department of Pediatrics, 2nd Medical Faculty, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Anna Křepelová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Milan Macek
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
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Fan H, Xu Y, Zhao Y, Feng K, Hong L, Zhao Q, Lu X, Shi M, Li H, Wang L, Wen S. Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis. Forensic Sci Int Genet 2024; 71:103029. [PMID: 38518712 DOI: 10.1016/j.fsigen.2024.103029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 02/12/2024] [Accepted: 03/03/2024] [Indexed: 03/24/2024]
Abstract
Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.
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Affiliation(s)
- Haoliang Fan
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
| | - Yiran Xu
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China.
| | - Yutao Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Kai Feng
- Duanzhou Branch of Zhaoqing Public Security Bureau, Zhaoqing 526060, China.
| | - Liuxi Hong
- Sihui Public Security Bureau of Guangdong Province, Zhaoqing 526299, China.
| | - Qiancheng Zhao
- Public Security Bureau of Zhaoqing Municipality, Zhaoqing 526000, China.
| | - Xiaoyu Lu
- Deepreads Biotech Company Limited, Guangzhou 510663, China.
| | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing 100088, China.
| | - Haiyan Li
- Criminal Technology Center of Guangdong Provincial Public Security Department, Guangzhou 510050, China.
| | - Lingxiang Wang
- MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
| | - Shaoqing Wen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China; Institute of Archaeological Science, Fudan University, Shanghai 200433, China; MOE Laboratory for National Development and Intelligent Governance, Fudan University, Shanghai 200433, China.
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Gosch A, Banemann R, Dørum G, Haas C, Hadrys T, Haenggi N, Kulstein G, Neubauer J, Courts C. Spitting in the wind?-The challenges of RNA sequencing for biomarker discovery from saliva. Int J Legal Med 2024; 138:401-412. [PMID: 37847308 PMCID: PMC10861700 DOI: 10.1007/s00414-023-03100-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/25/2023] [Indexed: 10/18/2023]
Abstract
Forensic trace contextualization, i.e., assessing information beyond who deposited a biological stain, has become an issue of great and steadily growing importance in forensic genetic casework and research. The human transcriptome encodes a wide variety of information and thus has received increasing interest for the identification of biomarkers for different aspects of forensic trace contextualization over the past years. Massively parallel sequencing of reverse-transcribed RNA ("RNA sequencing") has emerged as the gold standard technology to characterize the transcriptome in its entirety and identify RNA markers showing significant expression differences not only between different forensically relevant body fluids but also within a single body fluid between forensically relevant conditions of interest. Here, we analyze the quality and composition of four RNA sequencing datasets (whole transcriptome as well as miRNA sequencing) from two different research projects (the RNAgE project and the TrACES project), aiming at identifying contextualizing forensic biomarker from the forensically relevant body fluid saliva. We describe and characterize challenges of RNA sequencing of saliva samples arising from the presence of oral bacteria, the heterogeneity of sample composition, and the confounding factor of degradation. Based on these observations, we formulate recommendations that might help to improve RNA biomarker discovery from the challenging but forensically relevant body fluid saliva.
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Affiliation(s)
- Annica Gosch
- Institute of Legal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Regine Banemann
- Federal Criminal Police Office, Forensic Science Institute, Wiesbaden, Germany
| | - Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Thorsten Hadrys
- State Criminal Police Office, Forensic Science Institute, Munich, Germany
| | - Nadescha Haenggi
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Galina Kulstein
- Federal Criminal Police Office, Forensic Science Institute, Wiesbaden, Germany
| | - Jacqueline Neubauer
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Cornelius Courts
- Institute of Legal Medicine, University Hospital of Cologne, Cologne, Germany.
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Zupanič Pajnič I, Leskovar T, Črešnar M. Improving kinship probability in analysis of ancient skeletons using identity SNPs and MPS technology. Int J Legal Med 2023:10.1007/s00414-023-03003-3. [PMID: 37127762 DOI: 10.1007/s00414-023-03003-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
In forensic kinship analysis and human identification cases, analysis of STRs is the gold standard. When badly preserved ancient DNA is used for kinship analysis, short identity SNPs are more promising for successful amplification. In this work, kinship analysis was performed on two skeletons from the Early Middle Ages. The surface contaminants of petrous bones were removed by chemical cleaning and UV irradiation; DNA was isolated through full demineralization and purified in an EZ1 Advanced XL machine. The PowerQuant kit was used to analyze DNA yield and degradation, and on average, 17 ng DNA/g of petrous bone was obtained. Both skeletons were typed in duplicate for STR markers using the Investigator EssplexPlus SE QS kit, and comparison of partial consensus genotypes showed shared allelic variants at most loci amplified, indicating close kinship. After statistical calculation, the full-sibling kinship probability was too low for kinship confirmation, and additional analyses were performed with PCR-MPS using the Precision ID Identity Panel. The HID Ion Chef Instrument was used to prepare the libraries and for templating and the Ion GeneStudio S5 System for sequencing. Analysis of identity SNPs produced full genetic profiles from both skeletons. For combined likelihood ratio (LR) calculation, the product rule was used, combining LR for STRs and LR for SNPs, and a combined LR of 3.3 × 107 (corresponding to a full-sibling probability of 99.999997%) was calculated. Through the SNP PCR-MPS that followed the STR analysis, full-sibling kinship between the ancient skeletons excavated from an early medieval grave was confirmed.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| | - Matija Črešnar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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Du Q, Ma G, Lu C, Wang Q, Fu L, Cong B, Li S. Development and evaluation of a novel panel containing 188 microhaplotypes for 2nd-degree kinship testing in the Hebei Han population. Forensic Sci Int Genet 2023; 65:102855. [PMID: 36947934 DOI: 10.1016/j.fsigen.2023.102855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Distant kinship identification is one of the critical problems in forensic genetics. As a new type of genetic marker defined and discussed in the last decade, the microhaplotype (MH) has drawn much attention in such identification owing to its specific advantages to traditional short tandem repeat (STR) or single nucleotide polymorphism (SNP) markers. In this study, MH markers were screened step by step from the 1000 Genomes Project database, and a novel multiplex panel containing 188 MHs (in which 181 are reported the first time, while 1 was reported in a previous study and the other 6 have partial overlaps with known markers) was constructed for application in 2nd- and 3rd-degree kinship identification. Along with the construction, a novel MH nomenclature was proposed, in which the SNP position information they contained was taken into account to eliminate the possibility that the same locus was named differently interlaboratory. After a series of evaluations, the panel was shown to have good sequencing accuracy, high sensitivity, species specificity, and resistance to anti-PCR inhibitors or degradation. Population data of the 188 MHs were calculated based on the genetic information of 221 unrelated Hebei Han individuals, and the effective number of alleles (Ae) ranged from 2.0925 to 8.2634 (with an average of 2.9267). For the whole system, the cumulative matching probability (CMP), the cumulative power of exclusion in paternity testing of duos (CPEduo) and that of trios (CPEtrio) reached 2.8422 × 10-137, 1-1.3109 × 10-21, and 1-2.8975 × 10-39, respectively, indicating that this panel was satisfactory for individual identification and paternity testing. Then, the efficiency of the 188 MHs in 2nd- and 3rd-degree kinship testing was studied based on 30 extended families consisting of 179 2nd-degree and 121 3rd-degree relatives, as well as simulations of 0.5 million pairs of those two kinships. The results showed that clear opinions would be given in 83.36% of 2nd-degree identifications with a false rate less than 10-5, when the confirming and excluding thresholds of cumulative likelihood ratio (CLR) were set as 104 and 10-4, respectively. This panel is still not sufficient to solve the problem of 3rd-degree kinship identification alone, and approximately 300 or 870 MH loci would be needed in 2nd- or 3rd-degree kinship identification, respectively, to achieve a system efficiency not less than 0.99 with such a threshold set; such necessary numbers would be used only as a reference in further research.
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Affiliation(s)
- Qingqing Du
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Guanju Ma
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Chaolong Lu
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Qian Wang
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Lihong Fu
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Bin Cong
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China
| | - Shujin Li
- Hebei Key Laboratory of Forensic Medicine, College of Forensic Medicine, Hebei Medical University, Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, No. 361 Zhong Shan Road, Shijiazhuang, Hebei, China.
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Wessolly M, Stephan-Falkenau S, Streubel A, Wiesweg M, Borchert S, Mairinger E, Kollmeier J, Reis H, Bauer T, Schmid KW, Mairinger T, Schuler M, Mairinger FD. Digital gene expression analysis of NSCLC-patients reveals strong immune pressure, resulting in an immune escape under immunotherapy. BMC Cancer 2022; 22:46. [PMID: 34996407 PMCID: PMC8740040 DOI: 10.1186/s12885-021-09111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) are currently one of the most promising therapy options in the field of oncology. Although the first pivotal ICI trial results were published in 2011, few biomarkers exist to predict their therapy outcome. PD-L1 expression and tumor mutational burden (TMB) were proven to be sometimes-unreliable biomarkers. We have previously suggested the analysis of processing escapes, a qualitative measurement of epitope structure alterations under immune system pressure, to provide predictive information on ICI response. Here, we sought to further validate this approach and characterize interactions with different forms of immune pressure. METHODS We identified a cohort consisting of 48 patients with advanced non-small cell lung cancer (NSCLC) treated with nivolumab as ICI monotherapy. Tumor samples were subjected to targeted amplicon-based sequencing using a panel of 22 cancer-associated genes covering 98 mutational hotspots. Altered antigen processing was predicted by NetChop, and MHC binding verified by NetMHC. The NanoString nCounter® platform was utilized to provide gene expression data of 770 immune-related genes. Patient data from 408 patients with NSCLC were retrieved from The Cancer Genome Atlas (TCGA) as a validation cohort. RESULTS The two immune escape mechanisms of PD-L1 expression (TPS score) (n = 18) and presence of altered antigen processing (n = 10) are mutually non-exclusive and can occur in the same patient (n = 6). Both mechanisms have exclusive influence on different genes and pathways, according to differential gene expression analysis and gene set enrichment analysis, respectively. Interestingly, gene expression patterns associated with altered processing were enriched in T cell and NK cell immune activity. Though both mechanisms influence different genes, they are similarly linked to increased immune activity. CONCLUSION Pressure from the immune system will lay the foundations for escape mechanisms, leading to acquisition of resistance under therapy. Both PD-L1 expression and altered antigen processing are induced similarly by pronounced immunoactivity but in different context. The present data help to deepen our understanding of the underlying mechanisms behind those immune escapes.
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Affiliation(s)
- Michael Wessolly
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstrasse 55, 45147, Essen, Germany.
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Hufelandstrasse 55, 45147, Essen, Germany.
| | | | - Anna Streubel
- Department of Tissue Diagnostics, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Marcel Wiesweg
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Hufelandstrasse 55, 45147, Essen, Germany
| | - Sabrina Borchert
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstrasse 55, 45147, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Hufelandstrasse 55, 45147, Essen, Germany
| | - Elena Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstrasse 55, 45147, Essen, Germany
| | - Jens Kollmeier
- Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Henning Reis
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstrasse 55, 45147, Essen, Germany
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Torsten Bauer
- Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstrasse 55, 45147, Essen, Germany
| | - Thomas Mairinger
- Department of Tissue Diagnostics, Helios Klinikum Emil von Behring, Berlin, Germany
| | - Martin Schuler
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Hufelandstrasse 55, 45147, Essen, Germany
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, Hufelandstrasse 55, 45147, Essen, Germany
| | - Fabian D Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Hufelandstrasse 55, 45147, Essen, Germany
- German Cancer Consortium (DKTK), Partner Site University Hospital Essen, Hufelandstrasse 55, 45147, Essen, Germany
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8
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Maia N, Nabais Sá MJ, Melo-Pires M, de Brouwer APM, Jorge P. Intellectual disability genomics: current state, pitfalls and future challenges. BMC Genomics 2021; 22:909. [PMID: 34930158 PMCID: PMC8686650 DOI: 10.1186/s12864-021-08227-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Intellectual disability (ID) can be caused by non-genetic and genetic factors, the latter being responsible for more than 1700 ID-related disorders. The broad ID phenotypic and genetic heterogeneity, as well as the difficulty in the establishment of the inheritance pattern, often result in a delay in the diagnosis. It has become apparent that massive parallel sequencing can overcome these difficulties. In this review we address: (i) ID genetic aetiology, (ii) clinical/medical settings testing, (iii) massive parallel sequencing, (iv) variant filtering and prioritization, (v) variant classification guidelines and functional studies, and (vi) ID diagnostic yield. Furthermore, the need for a constant update of the methodologies and functional tests, is essential. Thus, international collaborations, to gather expertise, data and resources through multidisciplinary contributions, are fundamental to keep track of the fast progress in ID gene discovery.
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Affiliation(s)
- Nuno Maia
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal. .,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal.
| | - Maria João Nabais Sá
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Manuel Melo-Pires
- Serviço de Neuropatologia, Centro Hospitalar e Universitário do Porto (CHUPorto), Porto, Portugal
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Paula Jorge
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
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9
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Casals F, Rasal R, Anglada R, Tormo M, Bonet N, Rivas N, Vásquez P, Calafell F. A forensic population database in El Salvador: 58 STRs and 94 SNPs. Forensic Sci Int Genet 2021; 57:102646. [PMID: 34875492 DOI: 10.1016/j.fsigen.2021.102646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 12/31/2022]
Abstract
We have genotyped the 58 STRs (27 autosomal, 24 Y-STRs and 7 X-STRs) and 94 autosomal SNPs in Illumina ForenSeq™ Primer Mix A in a sample of 248 men and 143 women from El Salvador, Central America. Regional division (Centro, Oriente, Occidente) showed in almost all cases FST values not significantly different from 0, and further analyses were applied only to the undivided, country-wide population. The overall random match probability (RMP) decreased from 6.79 × 10-31 in length-based genotypes in the 27 autosomal STRs to 1.47 × 10-34 in repeat-sequence based genotypes. Combining the autosomal loci in this set, RMP reaches 2.97 × 10-70. In a population genetic analysis, El Salvador showed the lowest FST values with US Hispanics both for autosomal and X-STRs; however, it was much closer to Native Americans for the latter than for the former, in accordance with the well-known gender-biased admixture that created most Latin American populations.
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Affiliation(s)
- Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Departament de Genètica, Microbiologia i Estadísitca, Universitat de Barcelona, Barcelona, Spain
| | - Raquel Rasal
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Roger Anglada
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Marc Tormo
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain; Scientific IT Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Núria Bonet
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Catalonia, Spain
| | - Nury Rivas
- Instituto de Medicina Legal Dr. Roberto Masferrer, San Salvador, El Salvador
| | - Patricia Vásquez
- Asociación Pro-Búsqueda de Niñas y Niños Desaparecidos de El Salvador, 27 calle Pnte. No.1329 Colonia Layco, San Salvador, El Salvador
| | - Francesc Calafell
- Institute of Evolutionary Biology (UPF-CSIC), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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10
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Fan H, Wang L, Liu C, Lu X, Xu X, Ru K, Qiu P, Liu C, Wen SQ. Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing. Int J Legal Med 2021. [PMID: 34741666 DOI: 10.1007/s00414-021-02738-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
Short tandem repeats (STRs) are the preferred genetic markers in forensic DNA analysis, routinely measured by capillary electrophoresis (CE) method based on the fragment length features. While, the massive parallel sequencing (MPS) technology could simultaneously target a large number of intriguing forensic STRs, bypassing the intrinsic limitations of amplicon size separation and accessible fluorophores in CE, which is efficient and promising for enabling the identification of forensic biological evidence. Here, we developed a novel MPS-based Forensic Analysis System Multiplecues SetB Kit of 133-plex forensic STR markers (52 STRs and 81 Y-STRs) and one Y-InDel (M175) based on multiplex PCR and single-end 400 bp sequencing strategy. This panel was subjected to developmental validation studies according to the SWGDAM Validation Guidelines. Approximately 2185 MPS-based reactions using 6 human DNA standards and 8 male donors were conducted for substrate studies (filter paper, gauze, cotton swab, four different types of FTA cards, peripheral venous blood, saliva, and exfoliated cells), sensitivity studies (from 2 ng down to 0.0625 ng), mixture studies (two-person DNA mixtures), PCR inhibitor studies (seven commonly encountered PCR inhibitors), species specificity studies (11 non-human species), and repeatability studies. Results of concordance studies (413 Han males and 6 human DNA standards) generated by STRait Razor and in-house Python scripts indicated 99.98% concordance rate in STR calling relative to CE for STRs between 41,900 genotypes at 100 STR markers. Moreover, the limitations of present studies, the nomenclature rules and forensic MPS applications were also described. In conclusion, the validation studies based on ~ 2200 MPS-based and ~ 2500 CE-based DNA profiles demonstrated that the novel MPS-based panel meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities, and the STR nomenclature rules should be further regulated to integrate the inconformity between MPS-based and CE-based methods.
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11
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Leitao Braga B, Lisboa Gomes N, Nishi MY, Freire BL, Batista RL, D Faria Junior JA, Funari MFA, Figueredo Benedetti AF, de Moraes Narcizo A, Cavalca Cardoso L, Lerario AM, Guerra-Junior G, Frade Costa EM, Domenice S, Jorge AAL, Mendonca BB. Variants in 46,XY DSD-Related Genes in Syndromic and Non-Syndromic Small for Gestational Age Children with Hypospadias. Sex Dev 2021; 16:27-33. [PMID: 34518484 DOI: 10.1159/000518091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/23/2021] [Indexed: 11/19/2022] Open
Abstract
Hypospadias is a common congenital disorder of male genital formation. Children born small for gestational age (SGA) present a high frequency of hypospadias of undetermined etiology. No previous study investigated the molecular etiology of hypospadias in boys born SGA using massively parallel sequencing. Our objective is to report the genetic findings of a cohort of patients born SGA with medium or proximal hypospadias. We identified 46 individuals with this phenotype from a large cohort of 46,XY DSD patients, including 5 individuals with syndromic features. DNA samples from subjects were studied by either whole exome sequencing or target gene panel approach. Three of the syndromic patients have 5 main clinical features of Silver-Russell syndrome (SRS) and were first studied by MLPA. Among the syndromic patients, loss of DNA methylation at the imprinting control region H19/IGF2 was identified in 2 individuals with SRS clinical diagnosis. Two novel pathogenic variants in compound heterozygous state were identified in the CUL7 gene establishing the diagnosis of 3M syndrome in one patient, and a novel homozygous variant in TRIM37 was identified in another boy with Mulibrey nanism phenotype. Among the non-syndromic subjects, 7 rare heterozygous variants were identified in 6 DSD-related genes. However, none of the variants found can explain the phenotype by themselves. In conclusion, a genetic defect that clarifies the etiology of hypospadias was not found in most of the non-syndromic SGA children, supporting the hypothesis that multifactorial causes, new genes, and/or unidentified epigenetic defects may have an influence in this condition.
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Affiliation(s)
- Barbara Leitao Braga
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
| | - Nathalia Lisboa Gomes
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
| | - Mirian Y Nishi
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
| | - Bruna L Freire
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
| | - Rafael L Batista
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
| | - Jose A D Faria Junior
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
| | - Mariana F A Funari
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
| | - Anna F Figueredo Benedetti
- Laboratorio de Sequenciamento em Larga Escala (SELA), Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Amanda de Moraes Narcizo
- Laboratorio de Sequenciamento em Larga Escala (SELA), Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Lais Cavalca Cardoso
- Laboratorio de Sequenciamento em Larga Escala (SELA), Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | - Elaine M Frade Costa
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
| | - Sorahia Domenice
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil.,Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Berenice B Mendonca
- Unidade de Endocrinologia do Desenvolvimento - LIM/42, Hospital das Clinicas, Disciplina de Endocrinologia da FMUSP, Sao Paulo, Brazil
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12
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Faccinetto C, Sabbatini D, Serventi P, Rigato M, Salvoro C, Casamassima G, Margiotta G, De Fanti S, Sarno S, Staiti N, Luiselli D, Marino A, Vazza G. Internal validation and improvement of mitochondrial genome sequencing using the Precision ID mtDNA Whole Genome Panel. Int J Legal Med 2021; 135:2295-2306. [PMID: 34491421 PMCID: PMC8523450 DOI: 10.1007/s00414-021-02686-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/13/2021] [Indexed: 12/26/2022]
Abstract
With the recent advances in next-generation sequencing (NGS), mitochondrial whole-genome sequencing has begun to be applied to the field of the forensic biology as an alternative to the traditional Sanger-type sequencing (STS). However, experimental workflows, commercial solutions, and output data analysis must be strictly validated before being implemented into the forensic laboratory. In this study, we performed an internal validation for an NGS-based typing of the entire mitochondrial genome using the Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific) on the Ion S5 sequencer (Thermo Fisher Scientific). Concordance, repeatability, reproducibility, sensitivity, and heteroplasmy detection analyses were assessed using the 2800 M and 9947A standard control DNA as well as typical casework specimens, and results were compared with conventional Sanger sequencing and another NGS sequencer in a different laboratory. We discuss the strengths and limitations of this approach, highlighting some issues regarding noise thresholds and heteroplasmy detection, and suggesting solutions to mitigate these effects and improve overall data interpretation. Results confirmed that the Precision ID Whole mtDNA Genome Panel is highly reproducible and sensitive, yielding useful full mitochondrial DNA sequences also from challenging DNA specimens, thus providing further support for its use in forensic practice.
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Affiliation(s)
- Christian Faccinetto
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy.
| | - Daniele Sabbatini
- Department of Neurosciences DNS, University of Padova, Padova, Italy
| | - Patrizia Serventi
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Martina Rigato
- Department of Biology, University of Padova, Padova, Italy
| | | | - Gianluca Casamassima
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Gianluca Margiotta
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Sara De Fanti
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy.,Interdepartmental Centre Alma Mater Research Institute On Global Challenges and Climate Change (Alma Climate), University of Bologna, Bologna, Italy
| | - Stefania Sarno
- Department of Biological Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Nicola Staiti
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Alberto Marino
- Reparto Carabinieri Investigazioni Scientifiche Di Parma, Sezione Biologia, Parma, Italy
| | - Giovanni Vazza
- Department of Biology, University of Padova, Padova, Italy.
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13
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Wallander K, Thutkawkorapin J, Sahlin E, Lindblom A, Lagerstedt-Robinson K. Massive parallel sequencing in a family with rectal cancer. Hered Cancer Clin Pract 2021; 19:23. [PMID: 33827643 PMCID: PMC8028209 DOI: 10.1186/s13053-021-00181-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/30/2021] [Indexed: 12/29/2022] Open
Abstract
Background We have previously reported a family with a suspected autosomal dominant rectal and gastric cancer syndrome without any obvious causative genetic variant. Here, we focused the study on a potentially isolated rectal cancer syndrome in this family. Methods We included seven family members (six obligate carriers). Whole-exome sequencing and whole-genome sequencing data were analyzed and filtered for shared coding and splicing sequence and structural variants among the affected individuals. Results When considering family members with rectal cancer or advanced adenomas as affected, we found six new potentially cancer-associated variants in the genes CENPB, ZBTB20, CLINK, LRRC26, TRPM1, and NPEPL1. All variants were missense variants and none of the genes have previously been linked to inherited rectal cancer. No structural variant was found. Conclusion By massive parallel sequencing in a family suspected of carrying a highly penetrant rectal cancer predisposing genetic variant, we found six genetic missense variants with a potential connection to the rectal cancer in this family. One of them could be a high-risk genetic variant, or one or more of them could be low risk variants. The p.(Glu438Lys) variant in the CENPB gene was found to be of particular interest. The CENPB protein binds DNA and helps form centromeres during mitosis. It is involved in the WNT signaling pathway, which is critical for colorectal cancer development and its role in inherited rectal cancer needs to be further examined. Supplementary Information The online version contains supplementary material available at 10.1186/s13053-021-00181-2.
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Affiliation(s)
- Karin Wallander
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Jessada Thutkawkorapin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden. .,Department of Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden.
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Solna, Stockholm, Sweden
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14
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Davidson B, Kleinberg L, Børresen IM, Slettevoll F, Fangberget A, Hindosh D, Zahl Eriksson AG, Bjerkehagen B. Primary uterine ectomesenchymoma harboring a DICER1 mutation: case report with molecular analysis. Virchows Arch 2021; 479:419-424. [PMID: 33595736 PMCID: PMC8364549 DOI: 10.1007/s00428-021-03057-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/31/2021] [Accepted: 02/07/2021] [Indexed: 01/08/2023]
Abstract
Ectomesenchymoma is an exceedingly rare biphasic malignant tumor characterized by the presence of mesenchymal and neuroectodermal elements. The majority of patients are infants or children. We describe the first case of this entity diagnosed as a primary uterine tumor. A 72-year-old female presented with post-menopausal bleeding. Dilatation and curettage showed irregular mesenchymal proliferation of uncertain nature. In the hysterectomy specimen, a myxoid spindle cell tumor with areas of skeletal muscle and neural differentiation was found in the uterus, with direct invasion of the small intestine, and biphasic differentiation into rhabdomyosarcoma and ganglioneuroblastoma was unequivocally seen in a lymph node metastasis. The morphological findings were validated by immunohistochemistry. Massive parallel sequencing identified TP53, PTEN, and DICER1 mutations in the tumor. This report describes the presence of ectomesenchymoma in an unusual primary organ and in an uncharacteristic age and presents novel data regarding the genetic characteristics of this tumor.
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Affiliation(s)
- Ben Davidson
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Montebello, N-0310, Oslo, Norway. .,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, N-0316, Oslo, Norway.
| | - Lilach Kleinberg
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Montebello, N-0310, Oslo, Norway
| | - Ida Marie Børresen
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Montebello, N-0310, Oslo, Norway
| | - Frøydis Slettevoll
- Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, N-0310, Oslo, Norway
| | - Anne Fangberget
- Department of Radiology, Oslo University Hospital, Norwegian Radium Hospital, N-0310, Oslo, Norway
| | - Dunia Hindosh
- Department of Radiology, Kalnes Hospital, Kalnesveien 300, 1714, Grålum, Norway
| | - Ane Gerda Zahl Eriksson
- Department of Gynecologic Oncology, Oslo University Hospital, Norwegian Radium Hospital, N-0310, Oslo, Norway
| | - Bodil Bjerkehagen
- Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Montebello, N-0310, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, N-0316, Oslo, Norway.,Institute of Oral Biology, University of Oslo, N-0310, Oslo, Norway
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15
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Gomes R, Spinola PDS, Brant AC, Matta BP, Nascimento CM, de Aquino Paes SM, Bonvicino CR, Dos Santos ACE, Moreira MAM. Prevalence of germline variants in consensus moderate-to-high-risk predisposition genes to hereditary breast and ovarian cancer in BRCA1/2-negative Brazilian patients. Breast Cancer Res Treat 2021; 185:851-61. [PMID: 33128190 DOI: 10.1007/s10549-020-05985-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/15/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE This study aimed to identify and classify genetic variants in consensus moderate-to-high-risk predisposition genes associated with Hereditary Breast and Ovarian Cancer Syndrome (HBOC), in BRCA1/2-negative patients from Brazil. METHODS The study comprised 126 index patients who met NCCN clinical criteria and tested negative for all coding exons and intronic flanking regions of BRCA1/2 genes. Multiplex PCR-based assays were designed to cover the complete coding regions and flanking splicing sites of six genes implicated in HBOC. Sequencing was performed on HiSeq2500 Genome Analyzer. RESULTS Overall, we identified 488 unique variants. We identified five patients (3.97%) that harbored pathogenic or likely pathogenic variants in four genes: ATM (1), CHEK2 (2), PALB2 (1), and TP53 (1). One hundred and thirty variants were classified as variants of uncertain significance (VUS), 10 of which were predicted to disrupt mRNA splicing (seven non-coding variants and three coding variants), while other six missense VUS were classified as probably damaging by prediction algorithms. CONCLUSION A detailed mutational profile of non-BRCA genes is still being described in Brazil. In this study, we contributed to filling this gap, by providing important data on the diversity of genetic variants in a Brazilian high-risk patient cohort. ATM, CHEK2, PALB2 and TP53 are well established as HBOC predisposition genes, and the identification of deleterious variants in such actionable genes contributes to clinical management of probands and relatives.
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16
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Zupanič Pajnič I, Fattorini P. Strategy for STR typing of bones from the Second World War combining CE and NGS technology: A pilot study. Forensic Sci Int Genet 2021; 50:102401. [PMID: 33171316 DOI: 10.1016/j.fsigen.2020.102401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/21/2020] [Accepted: 09/26/2020] [Indexed: 01/23/2023]
Abstract
The genetic identification of skeletal remains found in Second World War mass graves is complicated because of the poor quality of the samples. The aim of this study was to set up a workflow for STR typing of such samples combining PCR/CE and PCR/NGS technologies. To this end, 57 DNA samples from an equal number of 75-year-old femurs were studied. After a first round of PCR typing using GlobalFiler CE, 42 samples yielded a full profile and were therefore submitted to our standard workflow. The 15 samples that yielded no or a limited number (2-17/21) of autosomal STR markers as well four bone control samples that provided a full profile with the conventional PCR/CE test were typed in duplicate by the GlobalFiler NGS kit. Despite the degradation of the samples, which resulted in lower coverage and a lower % of on-target reads, reliable sequencing data were obtained from 16/19 samples. The use of a threshold of 30× for the locus call led to a consensus profile (cp) of 20-31/31 STR autosomal loci in 10 samples and to a cp of 8-10/31 loci in two samples, whereas the four control samples yielded a cp of 26-31/31 loci. Finally, the data of the NGS typing were combined with those of the CE typing. This last task allowed us to recover (on average) three alleles per sample and to increase the number of the heterozygous patterns in 37 cases. In total, the combined approach proposed here made possible the genetic typing of 65-100% of the autosomal STR markers in 10/15 (66.6 %) skeletal remains that yielded no or very poor results with the conventional PCR/CE approach. However, because several artefacts (such as allelic drop-out and allelic drop-in) were scored, the risk of mistyping cannot be neglected.
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17
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Melchionda F, Stanciu F, Buscemi L, Pesaresi M, Tagliabracci A, Turchi C. Searching the undetected mtDNA variants in forensic MPS data. Forensic Sci Int Genet 2020; 49:102399. [PMID: 33038616 DOI: 10.1016/j.fsigen.2020.102399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/27/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
The efficiency of MPS in forensic mtDNA analysis has been thoroughly proven, although a reliable and well established data evaluation still remains a critical point. Numerous bioinformatics tools have been developed, but most of them require specific operating systems and high costs, while free open-source programs with user-friendly interfaces are few. In this study, 43 full mtGenomes were sequenced using the Ion Personal Genome Machine™ (PGM™) System and analyzed utilizing the plug-in Variant Caller (TVC) of the Ion Torrent Software Suite and the mtDNA-Server (mDS), a free web-based mitochondrial analysis tool for MPS data. The outcomes of these two different analysis tools were compared to variants noted after manual inspection of the aligned reads performed using Integrative Genomics Viewer (IGV). The comparison highlighted the presence of thirty-nine discordant variant calls, which were resolved by Sanger sequencing that confirmed the presence of all variants, except for 7 deletions. The combined adoption of IGV and Sanger type sequencing confirmatory steps, in addition of TVC and mDS analysis, resulted in a more accurate variants assignment with the detection of 32 additional true polymorphisms, which were noted in the final dataset. Regarding the heteroplasmy issue, out of a total of thirty heteroplasmic variants, twenty-eight were detected by the TVC, while the mDS detected twenty-two. Overall, none of the used bioinformatics tools were the perfect choice and a secondary analysis with an expert's opinion in complete mtGenome MPS data evaluation is still required in forensic genetic analysis.
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Affiliation(s)
- Filomena Melchionda
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Florin Stanciu
- Romanian National DNA Database, National Forensic Science Institute, General Inspectorate of Romanian Police, Bucharest, Romania.
| | - Loredana Buscemi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Mauro Pesaresi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Adriano Tagliabracci
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
| | - Chiara Turchi
- Section of Legal Medicine, Department of Excellence of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy - Via Tronto, 60126 Torrette Ancona, Italy.
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18
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Cavalheiro CP, Avila E, Gastaldo AZ, Graebin P, Motta CHA, Rodenbusch R, Alho CS. Uniparental disomy of chromosome 21: A statistical approach and application in paternity tests. Forensic Sci Int Genet 2020; 49:102368. [PMID: 32911454 DOI: 10.1016/j.fsigen.2020.102368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/30/2020] [Accepted: 07/31/2020] [Indexed: 11/24/2022]
Abstract
Considering the overall frequency of paternity investigation cases including mutational events, there is a real possibility that at least a fraction of all inconsistencies reported in paternity cases are caused not by polymerase slippage mutations, but to chromosomic abnormalities, as Uniparental Disomy (UPD). We report here the investigation of a trio paternity case (mother, child and alleged father), with observed inconsistencies that can alternatively be explained by occurrence of maternal uniparental isodisomy of chromosome 21 (miUPD21). A total of 350 short tandem repeat (STR) and single nucleotide polymorphism (SNP) markers were tested, statistically suggesting true biological linkage within the trio. Additionally, we propose miUPD21 explains, with significantly greater probability, the occurrence of detected inconsistencies, when compared to alternative hypothesis of multiple and simultaneous slippage mutations. Similar cases could have their statistical conclusions improved or even altered by including unusual chromosomal segregation patterns in the hypothesis formulation, as well as in mathematical calculations. Such reports of allelic inconsistencies being explained by chromosomal alterations are common in clinical genetics, and such situations might have impact on forensic investigation.
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Affiliation(s)
- C P Cavalheiro
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil.
| | - E Avila
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil; Polícia Federal, Setor Técnico Científico, Porto Alegre, RS, Brazil
| | - A Z Gastaldo
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil
| | - P Graebin
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil
| | - C H A Motta
- Instituto de Medicina Social e Criminalística de São Paulo, São Paulo, SP, Brazil
| | - R Rodenbusch
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - C S Alho
- Laboratório de Genética Humana e Molecular
- Genética Forense, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil; Instituto Nacional de Ciência e Tecnologia - Ciências Forenses, Porto Alegre, RS, Brazil
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Poduval DB, Ognedal E, Sichmanova Z, Valen E, Iversen GT, Minsaas L, Lønning PE, Knappskog S. Assessment of tumor suppressor promoter methylation in healthy individuals. Clin Epigenetics 2020; 12:131. [PMID: 32859265 PMCID: PMC7455917 DOI: 10.1186/s13148-020-00920-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022] Open
Abstract
Background The number of tumor suppressor genes for which germline mutations have been linked to cancer risk is steadily increasing. However, while recent reports have linked constitutional normal tissue promoter methylation of BRCA1 and MLH1 to ovarian and colon cancer risk, the role of epigenetic alterations as cancer risk factors remains largely unknown, presenting an important area for future research. Currently, we lack fast and sensitive methods for assessment of promoter methylation status across known tumor suppressor genes. Results In this paper, we present a novel NGS-based approach assessing promoter methylation status across a large panel of defined tumor suppressor genes to base-pair resolution. The method omits the limitations related to commonly used array-approaches. Our panel includes 565 target regions covering the promoters of 283 defined tumor suppressors, selected by pre-specified criteria, and was applied for rapid targeted methylation-specific NGS. The feasibility of the method was assessed by analyzing normal tissue DNA (white blood cells, WBC) samples from 34 healthy postmenopausal women and by performing preliminary assessment of the methylation landscape of tumor suppressors in these individuals. The mean target coverage was 189.6x providing a sensitivity of 0.53%, sufficient for promoter methylation assessment of low-level methylated genes like BRCA1. Within this limited test-set, we detected 206 regions located in the promoters of 149 genes to be differentially methylated (hyper- or hypo-) at > 99% confidence level. Seven target regions in gene promoters (CIITA, RASSF1, CHN1, PDCD1LG2, GSTP1, XPA, and ZNF668) were found to be hyper-methylated in a minority of individuals, with a > 20 percent point difference in mean methylation across the region between individuals. In an exploratory hierarchical clustering analysis, we found that the individuals analyzed may be grouped into two main groups based on their WBC methylation profile across the 283 tumor suppressor gene promoters. Conclusions Methylation-specific NGS of our tumor suppressor panel, with detailed assessment of differential methylation in healthy individuals, presents a feasible method for identification of novel epigenetic risk factors for cancer.
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Affiliation(s)
- Deepak B Poduval
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Elisabet Ognedal
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway.,Present address: Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Zuzana Sichmanova
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.,Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Gjertrud T Iversen
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Laura Minsaas
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Per E Lønning
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Oncology, Haukeland University Hospital, Bergen, Norway
| | - Stian Knappskog
- K.G. Jebsen Center for Genome Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen, Norway. .,Department of Oncology, Haukeland University Hospital, Bergen, Norway.
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20
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Rudenskaya GE, Kadnikova VA, Ryzhkova OP, Bessonova LA, Dadali EL, Guseva DS, Markova TV, Khmelkova DN, Polyakov AV. KIF1A-related autosomal dominant spastic paraplegias (SPG30) in Russian families. BMC Neurol 2020; 20:290. [PMID: 32746806 PMCID: PMC7398351 DOI: 10.1186/s12883-020-01872-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
Background Spastic paraplegia type 30 (SPG30) caused by KIF1A mutations was first reported in 2011 and was initially considered a very rare autosomal recessive (AR) form. In the last years, thanks to the development of massive parallel sequencing, SPG30 proved to be a rather common autosomal dominant (AD) form of familial or sporadic spastic paraplegia (SPG),, with a wide range of phenotypes: pure and complicated. The aim of our study is to detect AD SPG30 cases and to examine their molecular and clinical characteristics for the first time in the Russian population. Methods Clinical, genealogical and molecular methods were used. Molecular methods included massive parallel sequencing (MPS) of custom panel ‘spastic paraplegias’ with 62 target genes complemented by familial Sanger sequencing. One case was detected by the whole -exome sequencing. Results AD SPG30 was detected in 10 unrelated families, making it the 3rd (8.4%) most common SPG form in the cohort of 118 families. No AR SPG30 cases were detected. In total, 9 heterozygous KIF1A mutations were detected, with 4 novel and 5 known mutations. All the mutations were located within KIF1A motor domain. Six cases had pure phenotypes, of which 5 were familial, where 2 familial cases demonstrated incomplete penetrance, early onset and slow relatively benign SPG course. All 4 complicated cases were caused by novel mutations without familial history. The phenotypes varied from severe in two patients (e.g. lack of walking, pronounced mental retardation) to relatively mild non-disabling symptoms in two others. Conclusion AD SPG30 is one of the most common forms of SPG in Russia, the disorder has pronounced clinical variability while pure familial cases represent a significant part.
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Affiliation(s)
- G E Rudenskaya
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics" (RCMG), Moscow, Russia
| | - V A Kadnikova
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics" (RCMG), Moscow, Russia.
| | - O P Ryzhkova
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics" (RCMG), Moscow, Russia
| | - L A Bessonova
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics" (RCMG), Moscow, Russia
| | - E L Dadali
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics" (RCMG), Moscow, Russia
| | - D S Guseva
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics" (RCMG), Moscow, Russia
| | - T V Markova
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics" (RCMG), Moscow, Russia
| | | | - A V Polyakov
- Federal State Budgetary Scientific Institution "Research Centre for Medical Genetics" (RCMG), Moscow, Russia
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21
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Xavier C, de la Puente M, Phillips C, Eduardoff M, Heidegger A, Mosquera-Miguel A, Freire-Aradas A, Lagace R, Wootton S, Power D, Parson W, Lareu MV, Daniel R. Forensic evaluation of the Asia Pacific ancestry-informative MAPlex assay. Forensic Sci Int Genet 2020; 48:102344. [PMID: 32615397 DOI: 10.1016/j.fsigen.2020.102344] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/22/2020] [Accepted: 06/15/2020] [Indexed: 01/21/2023]
Abstract
DNA intelligence, and particularly the inference of biogeographical ancestry (BGA) is increasing in interest, and relevance within the forensic genetics community. The majority of current MPS-based forensic ancestry-informative assays focus on the differentiation of major global populations. The recently published MAPlex (Multiplex for the Asia Pacific) panel contains 144 SNPs and 20 microhaplotypes and aims to improve the differentiation of populations in the Asia Pacific region. This study reports the first forensic evaluation of the MAPlex panel using AmpliSeq technology and Ion S5 sequencing. This study reports on the overall performance of MAPlex including the assay's sequence coverage distribution and stability, baseline noise and description of problematic SNPs. Dilution series, artificially degraded and mixed DNA samples were also analysed to evaluate the sensitivity of the panel with challenging or compromised forensic samples. As the first panel to combine biallelic SNPs, multiple-allele SNPs and microhaplotypes, the MAPlex assay demonstrated an enhanced capacity for mixture detection, not easily performed with common binary SNPs. This performance evaluation indicates that MAPlex is a robust, stable and highly sensitive assay that is applicable to forensic casework for the prediction of BGA.
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Affiliation(s)
- C Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - M de la Puente
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - M Eduardoff
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - A Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - R Lagace
- Human Identification Group, Thermo Fisher Scientific, CA, USA
| | - S Wootton
- Human Identification Group, Thermo Fisher Scientific, CA, USA
| | - D Power
- Thermo Fisher Scientific, Victoria, Australia
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - R Daniel
- Office of the Chief Forensic Scientist, Forensic Services Department, Victoria Police, Macleod, Australia; National Centre for Forensic Studies, Faculty of Science & Technology, University of Canberra, ACT, Australia
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22
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Martin S, Smolders S, Van den Haute C, Heeman B, van Veen S, Crosiers D, Beletchi I, Verstraeten A, Gossye H, Gelders G, Pals P, Hamouda NN, Engelborghs S, Martin JJ, Eggermont J, De Deyn PP, Cras P, Baekelandt V, Vangheluwe P, Van Broeckhoven C; BELNEU consortium. Mutated ATP10B increases Parkinson's disease risk by compromising lysosomal glucosylceramide export. Acta Neuropathol 2020; 139:1001-24. [PMID: 32172343 DOI: 10.1007/s00401-020-02145-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023]
Abstract
Parkinson’s disease (PD) is a progressive neurodegenerative brain disease presenting with a variety of motor and non-motor symptoms, loss of midbrain dopaminergic neurons in the substantia nigra pars compacta and the occurrence of α-synuclein-positive Lewy bodies in surviving neurons. Here, we performed whole exome sequencing in 52 early-onset PD patients and identified 3 carriers of compound heterozygous mutations in the ATP10B P4-type ATPase gene. Genetic screening of a Belgian PD and dementia with Lewy bodies (DLB) cohort identified 4 additional compound heterozygous mutation carriers (6/617 PD patients, 0.97%; 1/226 DLB patients, 0.44%). We established that ATP10B encodes a late endo-lysosomal lipid flippase that translocates the lipids glucosylceramide (GluCer) and phosphatidylcholine (PC) towards the cytosolic membrane leaflet. The PD associated ATP10B mutants are catalytically inactive and fail to provide cellular protection against the environmental PD risk factors rotenone and manganese. In isolated cortical neurons, loss of ATP10B leads to general lysosomal dysfunction and cell death. Impaired lysosomal functionality and integrity is well known to be implicated in PD pathology and linked to multiple causal PD genes and genetic risk factors. Our results indicate that recessive loss of function mutations in ATP10B increase risk for PD by disturbed lysosomal export of GluCer and PC. Both ATP10B and glucocerebrosidase 1, encoded by the PD risk gene GBA1, reduce lysosomal GluCer levels, emerging lysosomal GluCer accumulation as a potential PD driver.
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23
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Isaksson S, Hazem B, Jönsson M, Reuterswärd C, Karlsson A, Griph H, Engleson J, Oskarsdottir G, Öhman R, Holm K, Rosengren F, Annersten K, Jönsson G, Borg Å, Edsjö A, Levéen P, Brunnström H, Lindquist KE, Staaf J, Planck M. Clinical Utility of Targeted Sequencing in Lung Cancer: Experience From an Autonomous Swedish Health Care Center. JTO Clin Res Rep 2020; 1:100013. [PMID: 34589915 PMCID: PMC8474272 DOI: 10.1016/j.jtocrr.2020.100013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES Mutation analysis by massive parallel sequencing (MPS) is routinely performed in the clinical management of lung cancer in Sweden. We describe the clinical and mutational profiles of lung cancer patients subjected to the first 1.5 years of treatment predictive MPS testing in an autonomous regional health care region. METHODS Tumors from all patients with lung cancer who had an MPS test from January 2015 to June 2016 in the Skåne health care region in Sweden (1.3 million citizens) were included. Six hundred eleven tumors from 599 patients were profiled using targeted sequencing with a 26-gene exon-focused panel. Data on disease patterns and characteristics of the patients subjected to testing were assembled, and correlations between mutational profiles and clinical features were analyzed. RESULTS MPS with the 26-gene panel revealed alterations in 92% of the 611 lung tumors, with the most frequent mutations detected in the nontargetable genes TP53 (62%) and KRAS (37%). Neither KRAS nor TP53 mutations were associated with disease pattern, chemotherapy response, progression-free survival, or overall survival in advanced-stage disease treated with platinum-based doublet chemotherapy as a first-line treatment. Among targetable genes, EGFR driver mutations were detected in 10% of the tumors, and BRAF p.V600 variants in 2.3%. For the 71 never smokers (12%), targetable alterations (EGFR mutations, BRAF p.V600, MET exon 14 skipping, or ALK/ROS1 rearrangement) were detected in 59% of the tumors. CONCLUSION Although the increasing importance of MPS as a predictor of response to targeted therapies is indisputable, its role in prognostics or as a predictor of clinical course in nontargetable advanced stage lung cancer requires further investigation.
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Affiliation(s)
- Sofi Isaksson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Bassam Hazem
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Mats Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Christel Reuterswärd
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Anna Karlsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Håkan Griph
- Department of Respiratory Medicine, Skane University Hospital, Lund, Sweden
| | - Jens Engleson
- Department of Oncology, Skane University Hospital, Lund, Sweden
| | - Gudrun Oskarsdottir
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Respiratory Medicine, Skane University Hospital, Lund, Sweden
| | - Ronny Öhman
- Department of Respiratory Medicine, Skane University Hospital, Lund, Sweden
| | - Karolina Holm
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Frida Rosengren
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Karin Annersten
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Åke Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Anders Edsjö
- Department of Pathology, Regional Laboratories Region Skane, Lund, Sweden
| | - Per Levéen
- Department of Pathology, Regional Laboratories Region Skane, Lund, Sweden
| | - Hans Brunnström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Pathology, Regional Laboratories Region Skane, Lund, Sweden
| | - Kajsa Ericson Lindquist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Pathology, Regional Laboratories Region Skane, Lund, Sweden
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Maria Planck
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Department of Respiratory Medicine, Skane University Hospital, Lund, Sweden
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Muñoz-Palazon B, Rodriguez-Sanchez A, Hurtado-Martinez M, Santana F, Gonzalez-Lopez J, Mack L, Gonzalez-Martinez A. Polar Arctic Circle biomass enhances performance and stability of aerobic granular sludge systems operated under different temperatures. Bioresour Technol 2020; 300:122650. [PMID: 31911317 DOI: 10.1016/j.biortech.2019.122650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
Three bioreactors were inoculated with Polar Arctic Circle-activated sludge, started-up and operated for 150 days at 8, 15 and 26 °C. Removal performances and granular conformation were similar at steady-state, but higher stability from start-up was found when operating at 8 °C. Important changes in the eukaryotic and prokaryotic populations caused by operational temperature were observed, being fungi dominant at 8 °C and 15 °C, while that ciliated organisms were found at 26 °C. The qPCR results showed higher copies of bacteria, and nitrifiers and denitrifying bacteria at cold temperature. The emission of nitrous oxide was linked directly with temperature and the involved microorganisms. This study represents a proof of concept in performance, greenhouse gas emission, granular formation and the role of the Polar Arctic Circle microbial population in AGS technology under different temperatures with the aim to understand the effect of seasonal o daily changes for implementation of AGS at full-scale.
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Affiliation(s)
- Bárbara Muñoz-Palazon
- Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, 18071 Granada, Spain.
| | | | - Miguel Hurtado-Martinez
- Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, 18071 Granada, Spain
| | - Francisco Santana
- Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, 18071 Granada, Spain
| | - Jesus Gonzalez-Lopez
- Institute of Water Research, University of Granada, C/Ramon y Cajal, 4, 18071 Granada, Spain
| | - Leoni Mack
- Department of Aquatic Ecology, University of Duisburg-Essen, Universitätsstraße 5, 45141 Essen, Germany
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Abstract
Non-invasive fetal HPA-1a typing is a valuable tool to identify the pregnancies at risk of fetal and neonatal alloimmune thrombocytopenia (FNAIT). At present, prenatal determination of the fetus HPA-1a type is performed for diagnostic purposes in pregnancies of HPA-1 alloimmunized women with history of a previous fetus or child with FNAIT. Different approaches have been used to determine the fetal HPA-1a genotype from cell-free fetal DNA (cffDNA) in the mother's plasma, mainly based on real-time PCR. Due to the single nucleotide polymorphism (SNP) between the HPA-1a and HPA-1b allelic sequences, a robust and accurate detection of the fetal genotype is challenging, and the sensitivity of most assays is still limited early in pregnancy. Nowadays, the availability of technologies such as next generation sequencing (NGS) or digital PCR offers unprecedented possibilities of analyzing cell-free DNA (cfDNA)-amplified sequences with very high coverage and high sensitivity. In addition, other interesting approaches using variant sequence enrichment strategies have been recently described. In particular, coamplification at lower denaturation temperature PCR (COLD-PCR) offers a simple and sensitive strategy for noninvasive fetal HPA-1 typing. These novel approaches are explained in more detail in this review. Despite no population-based FNAIT screening programs have so far been implemented, the perspectives in terms of treatment and prevention are changing and less costly high-throughput maternal HPA-1a typing methods have been developed. Altogether, this may lead to the implementation of fetal HPA-1a typing with a broader scope in the future, playing a critical role within FNAIT screening programs.
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Affiliation(s)
- Núria Nogués
- Immunohematology Laboratory, Banc de Sang i Teixits, Pg. Taulat 116, 08005 Barcelona, Spain; Department of Medicine, Universitat Autònoma de Barcelona, Passeig Vall d'Hebron 129-139, 08035 Barcelona, Spain.
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Naue J, Sänger T, Lutz-Bonengel S. Get it off, but keep it: Efficient cleaning of hair shafts with parallel DNA extraction of the surface stain. Forensic Sci Int Genet 2020; 45:102210. [PMID: 31812096 DOI: 10.1016/j.fsigen.2019.102210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 01/10/2023]
Abstract
The analysis of hair samples is a common task in forensic investigations. Material transferred to the surface of a hair during a crime challenges the analysis as it has to be removed efficiently. However, the removal of the stain can also lead to a loss of information on stain contributors. DNA analysis of the stain itself might thus be helpful for the forensic investigation. The aim of this study was the examination of different methods to remove common biological surface stains completely from human hair shafts without hampering the parallel DNA extraction of the cleaned hair shaft and the isolated surface stain (blood, saliva, vaginal secretion, semen, and skin flocks). Four different methods of cleaning (water, lysis buffer, swabbing, NaClO) were compared to their cleaning efficiency as well as their success of mtDNA analysis of three hair donors and the original five stains on the hair. In order to test the suitability of this procedure for future analysis methods, a selection of samples were also sequenced with MPS. Additionally, nuclear DNA analysis of the stain DNA was performed using a screening STR assay to test the potential success for detection of a STR profile. The most efficient removal of the stain was achieved using NaClO, however compromising further analysis of the stain DNA. The best results for cleaning and parallel stain analysis were obtained using a swab moistened with 0.5 % SDS for surface cleaning. Especially water failed to remove stains efficiently, leading to a high amount of mixed mtDNA in the DNA extracts. MPS showed an increased sensitivity for detection of minute mixtures.
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Dyrhovden R, Øvrebø KK, Nordahl MV, Nygaard RM, Ulvestad E, Kommedal Ø. Bacteria and fungi in acute cholecystitis. A prospective study comparing next generation sequencing to culture. J Infect 2019; 80:16-23. [PMID: 31586461 DOI: 10.1016/j.jinf.2019.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Guidelines for antibiotic treatment of acute cholecystitis are based on studies using culture techniques for microbial identification. Microbial culture has well described limitations and more comprehensive data on the microbial spectrum may support adjustments of these recommendations. We used next generation sequencing to conduct a thorough microbiological characterization of bile-samples from patients with moderate and severe acute cholecystitis. METHODS We prospectively included patients with moderate and severe acute cholecystitis, undergoing percutaneous or perioperative drainage of the gall bladder. Bile samples were analyzed using both culture and deep sequencing of bacterial 16S rRNA and rpoB genes and the fungal ITS2-segment. Clinical details were evaluated by medical record review. RESULTS Thirty-six patients with moderate and severe acute cholecystitis were included. Bile from 31 (86%) of these contained bacteria (29) and/or fungi (5) as determined by sequencing. Culture identified only 40 (38%) of the 106 microbes identified by sequencing. In none of the 15 polymicrobial samples did culture detect all present microbes. Frequently identified bacteria often missed by culture included oral streptococci, anaerobic bacteria, enterococci and Enterobacteriaceae other than Klebsiella spp. and Escherichia coli. CONCLUSIONS Culture techniques display decreased sensitivity for the microbial diagnostics of acute cholecystitis leaving possible pathogens undetected.
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Affiliation(s)
- Ruben Dyrhovden
- Department of Microbiology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway.
| | - Kjell Kåre Øvrebø
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | | | - Randi M Nygaard
- Department of Microbiology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway
| | - Elling Ulvestad
- Department of Microbiology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway; Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Øyvind Kommedal
- Department of Microbiology, Haukeland University Hospital, Jonas Lies vei 65, 5021 Bergen, Norway
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Chang L, Yu H, Miao X, Zhang J, Li S. Development and comprehensive evaluation of a noninvasive prenatal paternity testing method through a scaled trial. Forensic Sci Int Genet 2019; 43:102158. [PMID: 31479931 DOI: 10.1016/j.fsigen.2019.102158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 08/23/2019] [Accepted: 08/28/2019] [Indexed: 11/24/2022]
Abstract
PURPOSE To eliminate the miscarriage risks caused by traditional invasive sampling methods, we develop a noninvasive prenatal paternity testing (NIPPT) method and evaluate its efficiency, reliability and sensitivity based on a scaled trial. METHODS We use maternal cell-free DNA and massive parallel sequencing to obtain NIPPT genotypes for parents and fetuses based on quality-controlled genome-wide single nucleotide polymorphisms (SNPs). In a preliminary testing, data from 14 pregnant women and 7 negative controls are used for setting threshold of fetal genotyping in reference to postpartum children. After that, those from 349 cases with pregnancies of 6-35 gestational weeks (GW) and 9 negative controls from non-pregnant women who have fertility experience previously are in-depth evaluated. RESULTS In all cases, the biological fathers have been successfully identified from unrelated with a combined paternity index (CPI) of 3.58 × 1018 - 1.46 × 10165 for the cases versus 1.52 × 10-22 - 2.30 × 10-839 for the controls. For negative controls, fetal SNPs originating from previous pregnancies could not be detected. Our NIPPT results completely aligned with the invasive prenatal test results using PCR-CE STR methods. CONCLUSION NIPPT can be applied to determine paternity accurately from 6 weeks after conception until birth and may serve as an alternative prenatal paternity test advantageous to the currently-used methods.
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Affiliation(s)
- Liao Chang
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Huiyun Yu
- BGI-shenzhen, Shenzhen, 518083, China
| | - Xinyao Miao
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jianbo Zhang
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Shengbin Li
- College of Medicine and Forensics, Xi'an Jiaotong University, Xi'an, 710061, China; BGI-shenzhen, Shenzhen, 518083, China.
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Avila E, Graebin P, Chemale G, Freitas J, Kahmann A, Alho CS. Full mtDNA genome sequencing of Brazilian admixed populations: A forensic-focused evaluation of a MPS application as an alternative to Sanger sequencing methods. Forensic Sci Int Genet 2019; 42:154-164. [PMID: 31325893 DOI: 10.1016/j.fsigen.2019.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022]
Abstract
The use of Massive Parallel Sequencing (MPS) techniques have been proposed by the forensic community as an alternative to Sanger sequencing methods in routine forensic casework analysis regarding mitochondrial DNA (mtDNA). Interesting features of MPS include high throughput, ability to simultaneously genotype a significant number of samples by barcoding techniques, processing automation, reduced time and costs, among others. Advantages include the capability of generating full mtDNA genome sequences versus usual techniques, usually limited to hypervariable or control regions exclusively. In this work, 96 reference single-source samples from three different Brazilian cities were subjected to full mtDNA genome sequencing by MPS techniques using an early-access version of Precision ID mtDNA Whole Genome Panel on an Ion Torrent PGM platform (Thermo Fisher Scientific, Waltham, MA, USA). Complete, high-quality sequences were obtained and sequencing performance was evaluated via four different metrics. As a subset of evaluated samples have been previously submitted for Sanger sequencing of the control region, a comparative analysis of both methods' results was conducted in order to compare technique adequacy within a forensic context. Even though this study is one of the first to report full mtDNA genome sequences for Brazilian admixed populations, the observed haplotypes exhibit a predominance of Native American and African maternal lineages in the studied sample set, reproducing results described in the literature for control regions only. Interpopulation analysis among Brazilian and 26 worldwide populations was also carried out. The results indicate that MPS-generated full mtDNA genome sequences may have great utility in forensic real casework applications, with a pronounced gain of genetic information and discrimination power provided by coding region evaluation and the enhanced capacity of heteroplasmies determination. Database construction and other relevant factors concerning implementation of such techniques in Brazilian forensic laboratories are also discussed.
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Affiliation(s)
- E Avila
- Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil; Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil.
| | - P Graebin
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - G Chemale
- Setor Técnico-Científico, Superintendência Regional do Rio Grande do Sul, Polícia Federal, Porto Alegre, Brazil
| | - J Freitas
- Instituto Nacional de Criminalística, Polícia Federal, Brasília, DF, Brazil
| | - A Kahmann
- Instituto de Matemática, Estatística e Física, Universidade Federal de Rio Grande, Rio Grande, Brazil
| | - C S Alho
- Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Ciência e Tecnologia INCT Ciências Forenses, Porto Alegre, Brazil
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30
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Mertens J, Zambelli F, Daneels D, Caljon B, Sermon K, Spits C. Detection of Heteroplasmic Variants in the Mitochondrial Genome through Massive Parallel Sequencing. Bio Protoc 2019; 9:e3283. [PMID: 33654798 DOI: 10.21769/bioprotoc.3283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/21/2019] [Accepted: 05/23/2019] [Indexed: 11/02/2022] Open
Abstract
Detecting heteroplasmies in the mitochondrial DNA (mtDNA) has been a challenge for many years. In the past, Sanger sequencing was the main option to perform this analysis, however, this method could not detect low frequency heteroplasmies. Massive Parallel Sequencing (MPS) provides the opportunity to study the mtDNA in depth, but a controlled pipeline is necessary to reliably retrieve and quantify the low frequency variants. It has been shown that differences in methods can significantly affect the number and frequency of the retrieved variants. In this protocol, we present a method involving both wet lab and bioinformatics that allows identifying and quantifying single nucleotide variants in the full mtDNA sequence, down to a heteroplasmic load of 1.5%. For this, we set up a PCR-based amplification of the mtDNA, followed by MPS using Illumina chemistry, and variant calling with two different algorithms, mtDNA server and Mutect. The PCR amplification is used to enrich the mitochondrial fraction, while the bioinformatic processing with two algorithms is used to discriminate the true heteroplasmies from background noise. The protocol described here allows for deep sequencing of the mitochondrial DNA in bulk DNA samples as well as single cells (both large cells such as human oocytes, and small-sized single cells such as human embryonic stem cells) with minor modifications to the protocol.
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Affiliation(s)
- Joke Mertens
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussel, Belgium
| | | | - Dorien Daneels
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Ben Caljon
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussel, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussel, Belgium
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Nesti C, Rubegni A, Tolomeo D, Baldacci J, Cassandrini D, D'Amore F, Santorelli FM. Complex multisystem phenotype associated with the mitochondrial DNA m.5522G>A mutation. Neurol Sci 2019; 40:1705-1708. [PMID: 30937556 DOI: 10.1007/s10072-019-03864-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/21/2019] [Indexed: 02/07/2023]
Abstract
Mitochondrial tRNAs are responsible for more than half of pathogenic point mutations in the mitochondrial genome (mtDNA). Different mutations give rise to widely differing phenotypes, ranging from isolated organ-specific diseases to multisystem conditions. Herein, we report a 40-year-old woman presenting with a complex multisystem phenotype including sensorineural hearing loss, retinopathy, severe dilated cardiomyopathy, non-insulin dependent diabetes mellitus, and renal failure. Sequence analysis of mtDNA identified the m.5522G>A mutation in MT-TW, the gene encoding mitochondrial tRNA for tryptophan. The heteroplasmic variant, thus far described once, was almost exclusively confined to skeletal muscle tissue, as shown by massive parallel sequencing and corroborated by an ad hoc designed PCR-based strategy. This patient, presenting a severe, multisystem involvement apparently sparing the brain, contributes to the genetic heterogeneity of mitochondrial diseases caused by mutations in mitochondrial tRNAs.
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Affiliation(s)
- Claudia Nesti
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, via dei Giacinti 2, 56128, Pisa, Italy.
| | - Anna Rubegni
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, via dei Giacinti 2, 56128, Pisa, Italy
| | - Deborah Tolomeo
- Department of Clinical and Experimental Medicine, University of Pisa, via dei Giacinti 2, 56128, Calambrone, Pisa, Italy
| | - Jacopo Baldacci
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, via dei Giacinti 2, 56128, Pisa, Italy
| | - Denise Cassandrini
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, via dei Giacinti 2, 56128, Pisa, Italy
| | - Francesca D'Amore
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, via dei Giacinti 2, 56128, Pisa, Italy
| | - Filippo M Santorelli
- Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Stella Maris Foundation, via dei Giacinti 2, 56128, Pisa, Italy.
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Sonon P, Sadissou I, Tokplonou L, M'po KKG, Glitho SSC, Agniwo P, Ibikounlé M, Massaro JD, Massougbodji A, Moreau P, Sabbagh A, Mendes-Junior CT, Moutairou KA, Castelli EC, Courtin D, Donadi EA. HLA-G, -E and -F regulatory and coding region variability and haplotypes in the Beninese Toffin population sample. Mol Immunol 2018; 104:108-127. [PMID: 30448608 DOI: 10.1016/j.molimm.2018.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/16/2018] [Indexed: 12/17/2022]
Abstract
HLA-G/E/F genes exhibit immunomodulatory properties and are expressed in placenta. Little attention has been devoted to the study of these genes in sub-Saharan African populations, which are yet the most diverse. To fill this gap, we evaluated the complete gene variability, approximately 5.1 kb for HLA-G (n = 149), 7.7 kb for HLA-E (n = 150) and 6.2 kb for HLA-F (n = 152) in the remote Beninese Toffin population, using massive parallel sequencing. Overall, 96, 37 and 68 variable sites were detected along the entire HLA-G, -E and -F, respectively, arranged into region-specific haplotypes; i.e., promoter haplotypes (16, 19, and 15 respectively), coding haplotypes (19, 15, and 29 respectively), 3' untranslated region (3'UTR) haplotypes (12, 7 and 2, respectively) and extended haplotypes (33, 31 and 32 respectively). All promoter/coding/3'UTR haplotypes followed the patterns already described in worldwide populations. HLA-E was the most conserved, exhibiting mainly two full-length encoded-molecules (E*01:01 and E*01:03), followed by HLA-F, three full-length proteins (F*01:01, F*01:02 and F*01:03) and HLA-G, four proteins: three full-length (G*01:01, G*01:03 and G*01:04) and one truncated (G*01:05N). Although HLA-G/E/F alleles in the Toffin population were the most frequently observed worldwide, the frequencies of the coding haplotypes were closely similar to those described for other African populations (Guinea-Conakry and Burkina-Faso), when compared to non-African ones (Brazilian), indicating that variable sites along these genes were present in Africa before human dispersion.
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Affiliation(s)
- Paulin Sonon
- Laboratório de Biologia Molecular, Universidade de São Paulo, Programa de Imunologia Básica e Aplicada (IBA), Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Estado de São Paulo, SP, Brazil.
| | - Ibrahim Sadissou
- Laboratório de Biologia Molecular, Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Estado de São Paulo, SP, Brazil.
| | - Léonidas Tokplonou
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Benin; UMR 216 MERIT, IRD, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Université d'Abomey-Calavi, Cotonou, Benin.
| | - Kuumaaté K G M'po
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Benin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin.
| | - Sonya S C Glitho
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Benin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin.
| | - Privat Agniwo
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Benin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin.
| | - Moudachirou Ibikounlé
- Université d'Abomey-Calavi, Cotonou, Benin; Département de Zoologie, Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Benin.
| | - Juliana Doblas Massaro
- Laboratório de Biologia Molecular, Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Estado de São Paulo, SP, Brazil.
| | - Achille Massougbodji
- Centre d'Etude et de Recherche sur le Paludisme Associé à la Grossesse et à l'Enfance (CERPAGE), Faculté des Sciences de la Santé, Cotonou, Benin.
| | - Philippe Moreau
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Direction de la Recherche Fondamentale, Institut de Biologie François Jacob, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, Paris, France; Université Paris-Diderot, Sorbonne Paris-Cité, UMR_E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France.
| | - Audrey Sabbagh
- UMR 216 MERIT, IRD, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, State of São Paulo, Brazil.
| | - Kabirou A Moutairou
- Laboratoire de Biologie et Physiologie Cellulaire, Université d'Abomey-Calavi, Cotonou, Benin.
| | - Erick C Castelli
- São Paulo State University (UNESP), Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unit (UNIPEX), School of Medicine, Botucatu, State of São Paulo, Brazil; São Paulo State University (UNESP), Department of Pathology, School of Medicine, Botucatu, State of São Paulo, Brazil.
| | - David Courtin
- UMR 216 MERIT, IRD, Faculté de Pharmacie de Paris, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Eduardo A Donadi
- Laboratório de Biologia Molecular, Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto (FMRP-USP), Estado de São Paulo, SP, Brazil.
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Scheiper S, Ramos-Luis E, Blanco-Verea A, Niess C, Beckmann BM, Schmidt U, Kettner M, Geisen C, Verhoff MA, Brion M, Kauferstein S. Sudden unexpected death in the young - Value of massive parallel sequencing in postmortem genetic analyses. Forensic Sci Int 2018; 293:70-76. [PMID: 30415094 DOI: 10.1016/j.forsciint.2018.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/27/2018] [Accepted: 09/29/2018] [Indexed: 01/22/2023]
Abstract
Cases of sudden cardiac death (SCD) in young and apparently healthy individuals represent a devastating event in affected families. Hereditary arrhythmia syndromes, which include primary electrical heart disorders as well as cardiomyopathies, are known to contribute to a significant number of these sudden death cases. We performed postmortem genetic analyses in young sudden death cases (aged <45years) by means of a defined gene panel using massive parallel sequencing (MPS). The data were evaluated bioinformatically and detected sequence variants were assessed using common databases and applying in silico prediction tools. In this study, we identified variants with likely pathogenic effect in 6 of 9 sudden unexpected death (SUD) cases. Due to the detection of numerous unknown and unclassified variants, interpretation of the results proved to be challenging. However, by means of an appropriate evaluation of the findings, MPS represents an important tool to support the forensic investigation and implies great progress for relatives of young SCD victims facilitating adequate risk stratification and genetic counseling.
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Affiliation(s)
- Stefanie Scheiper
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt, Germany; German Red Cross Blood Center, Institute of Transfusion Medicine and Immunohaematology, University Hospital Frankfurt, Frankfurt, Germany.
| | - Eva Ramos-Luis
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela (A Coruña), Spain; Medicina Xenómica, Universidade de Santiago de Compostela-Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela (A Coruña), Spain
| | - Alejandro Blanco-Verea
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela (A Coruña), Spain; Medicina Xenómica, Universidade de Santiago de Compostela-Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela (A Coruña), Spain
| | - Constanze Niess
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Britt-Maria Beckmann
- Department of Medicine I, University Hospital Munich, Ludwig Maximilians University, Munich, Germany
| | - Ulrike Schmidt
- Institute of Legal Medicine, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mattias Kettner
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Christof Geisen
- German Red Cross Blood Center, Institute of Transfusion Medicine and Immunohaematology, University Hospital Frankfurt, Frankfurt, Germany
| | - Marcel A Verhoff
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Maria Brion
- Xenética Cardiovascular, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela (A Coruña), Spain; Medicina Xenómica, Universidade de Santiago de Compostela-Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela (A Coruña), Spain
| | - Silke Kauferstein
- Institute of Legal Medicine, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
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Oliveira M, Amorim A. Microbial forensics: new breakthroughs and future prospects. Appl Microbiol Biotechnol 2018; 102:10377-10391. [PMID: 30302518 PMCID: PMC7080133 DOI: 10.1007/s00253-018-9414-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 12/17/2022]
Abstract
Recent advances in genetic data generation, through massive parallel sequencing (MPS), storage and analysis have fostered significant progresses in microbial forensics (or forensic microbiology). Initial applications in circumstances of biocrime, bioterrorism and epidemiology are now accompanied by the prospect of using microorganisms (i) as ancillary evidence in criminal cases; (ii) to clarify causes of death (e.g., drownings, toxicology, hospital-acquired infections, sudden infant death and shaken baby syndromes); (iii) to assist human identification (skin, hair and body fluid microbiomes); (iv) for geolocation (soil microbiome); and (v) to estimate postmortem interval (thanatomicrobiome and epinecrotic microbial community). When compared with classical microbiological methods, MPS offers a diverse range of advantages and alternative possibilities. However, prior to its implementation in the forensic context, critical efforts concerning the elaboration of standards and guidelines consolidated by the creation of robust and comprehensive reference databases must be undertaken.
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Affiliation(s)
- Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal. .,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Júlio Amaral de Carvalho,45, 4200-135, Porto, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4200-135, Porto, Portugal.
| | - António Amorim
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Júlio Amaral de Carvalho,45, 4200-135, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4200-135, Porto, Portugal
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Hanssen EN, Liland KH, Gill P, Snipen L. Optimizing body fluid recognition from microbial taxonomic profiles. Forensic Sci Int Genet 2018; 37:13-20. [PMID: 30071492 DOI: 10.1016/j.fsigen.2018.07.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 12/17/2022]
Abstract
In forensics the DNA-profile is used to identify the person who left a biological trace, but information on body fluid can also be essential in the evidence evaluation process. Microbial composition data could potentially be used for body fluid recognition as an improved alternative to the currently used presumptive tests. We have developed a customized workflow for interpretation of bacterial 16S sequence data based on a model composed of Partial Least Squares (PLS) in combination with Linear Discriminant Analysis (LDA). Large data sets from the Human Microbiome Project (HMP) and the American Gut Project (AGP) were used to test different settings in order to optimize performance. From the initial cross-validation of body fluid recognition within the HMP data, the optimal overall accuracy was close to 98%. Sensitivity values for the fecal and oral samples were ≥0.99, followed by the vaginal samples with 0.98 and the skin and nasal samples with 0.96 and 0.81 respectively. Specificity values were high for all 5 categories, mostly >0.99. This optimal performance was achieved by using the following settings: Taxonomic profiles based on operational taxonomic units (OTUs) with 0.98 identity (OTU98), Aitchisons simplex transform with C = 1 pseudo-count and no regularization (r = 1) in the PLS step. Variable selection did not improve the performance further. To test for robustness across sequencing platforms, we also trained the classifier on HMP data and tested on the AGP data set. In this case, the standard OTU based approach showed moderately decline in accuracy. However, by using taxonomic profiles made by direct assignment of reads to a genus, we were able to nearly maintain the high accuracy levels. The optimal combination of settings was still used, except the taxonomic level being genus instead of OTU98. The performance may be improved even further by using higher resolution taxonomic bins.
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Affiliation(s)
- Eirik Nataas Hanssen
- Department of Forensic Biology, Oslo University Hospital, P.O. Box 4950 Nydalen, N-0424 Oslo, Norway; Department of Forensic Medicine, University of Oslo, P.O. Box 4950 Nydalen, N-0424 Oslo, Norway.
| | - Kristian Hovde Liland
- Faculty of Science and Technology, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway; Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway
| | - Peter Gill
- Department of Forensic Biology, Oslo University Hospital, P.O. Box 4950 Nydalen, N-0424 Oslo, Norway; Department of Forensic Medicine, University of Oslo, P.O. Box 4950 Nydalen, N-0424 Oslo, Norway
| | - Lars Snipen
- Faculty of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Ås, Norway.
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Brasil S, Leal F, Vega A, Navarrete R, Ecay MJ, Desviat LR, Riera C, Padilla N, de la Cruz X, Couce ML, Martin-Hernández E, Morais A, Pedrón C, Peña-Quintana L, Rigoldi M, Specola N, de Almeida IT, Vives I, Yahyaoui R, Rodríguez-Pombo P, Ugarte M, Pérez-Cerda C, Merinero B, Pérez B. Improving the diagnosis of cobalamin and related defects by genomic analysis, plus functional and structural assessment of novel variants. Orphanet J Rare Dis 2018; 13:125. [PMID: 30041674 PMCID: PMC6057060 DOI: 10.1186/s13023-018-0862-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/29/2018] [Indexed: 12/04/2022] Open
Abstract
Background Cellular cobalamin defects are a locus and allelic heterogeneous disorder. The gold standard for coming to genetic diagnoses of cobalamin defects has for some time been gene-by-gene Sanger sequencing of individual DNA fragments. Enzymatic and cellular methods are employed before such sequencing to help in the selection of the gene defects to be sought, but this is time-consuming and laborious. Furthermore some cases remain undiagnosed because no biochemical methods have been available to test for cobalamin absorption and transport defects. Results This paper reports the use of massive parallel sequencing of DNA (exome analysis) for the accurate and rapid genetic diagnosis of cobalamin-related defects in a cohort of affected patients. The method was first validated in an initial cohort with different cobalamin defects. Mendelian segregation, the frequency of mutations, and the comprehensive structural and functional analysis of gene variants, identified disease-causing mutations in 12 genes involved in the absorption and synthesis of active cofactors of vitamin B12 (22 cases), and in the non-cobalamin metabolism-related genes ACSF3 (in four biochemically misdiagnosed patients) and SUCLA2 (in one patient with an unusual presentation). We have identified thirteen new variants all classified as pathogenic according to the ACGM recommendation but four were classified as variant likely pathogenic in MUT and SUCLA2. Functional and structural analysis provided evidences to classify them as pathogenic variants. Conclusions The present findings suggest that the technology used is sufficiently sensitive and specific, and the results it provides sufficiently reproducible, to recommend its use as a second-tier test after the biochemical detection of cobalamin disorder markers in the first days of life. However, for accurate diagnoses to be made, biochemical and functional tests that allow comprehensive clinical phenotyping are also needed. Electronic supplementary material The online version of this article (10.1186/s13023-018-0862-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra Brasil
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Fátima Leal
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Ana Vega
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - María Jesús Ecay
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Lourdes R Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Casandra Riera
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Natàlia Padilla
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier de la Cruz
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Mari Luz Couce
- Hospital Clínico Universitario de Santiago, Santiago de Compostela, CIBERER, Santiago de Compostela, Spain
| | | | - Ana Morais
- Hospital Universitario La Paz, Madrid, Spain
| | | | - Luis Peña-Quintana
- Hospital Universitario Materno Infantil, CIBEROBN, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Miriam Rigoldi
- Center for Rare Disorders, ASST- Monza, Ospedale San Gerardo, Monza, Italy
| | - Norma Specola
- Unidad de Metabolismo Hospital de Niños de La Plata, La Plata, Argentina
| | | | | | - Raquel Yahyaoui
- Hospital Universitario Regional de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Celia Pérez-Cerda
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Begoña Merinero
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain.
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Naue J, Sänger T, Hoefsloot HCJ, Lutz-Bonengel S, Kloosterman AD, Verschure PJ. Proof of concept study of age-dependent DNA methylation markers across different tissues by massive parallel sequencing. Forensic Sci Int Genet 2018; 36:152-159. [PMID: 30031222 DOI: 10.1016/j.fsigen.2018.07.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022]
Abstract
The use of DNA methylation (DNAm) for chronological age determination has been widely investigated within the last few years for its application within the field of forensic genetics. The majority of forensic studies are based on blood, saliva, and buccal cell samples, respectively. Although these types of samples represent an extensive amount of traces found at a crime scene or are readily available from individuals, samples from other tissues can be relevant for forensic investigations. Age determination could be important for cases involving unidentifiable bodies and based on remaining soft tissue e.g. brain and muscle, or completely depend on hard tissue such as bone. However, due to the cell type specificity of DNAm, it is not evident whether cell type specific age-dependent CpG positions are also applicable for age determination in other cell types. Within this pilot study, we investigated whether 13 previously selected age-dependent loci based on whole blood analysis including amongst others ELOVL2, TRIM59, F5, and KLF14 also have predictive value in other forensically relevant tissues. Samples of brain, bone, muscle, buccal swabs, and whole blood of 29 deceased individuals (age range 0-87 years) were analyzed for these 13 age-dependent markers using massive parallel sequencing. Seven of these loci did show age-dependency in all five tissues. The change of DNAm during lifetime was different in the set of tissues analyzed, and sometimes other CpG sites within the loci showed a higher age-dependency. This pilot study shows the potential of existing blood DNAm markers for age-determination to analyze other tissues than blood. We identified seven known blood-based DNAm markers for use in muscle, brain, bone, buccal swabs, and blood. Nevertheless, a different reference set for each tissue is needed to adapt for tissue-specific changes of the DNAm over time.
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Affiliation(s)
- Jana Naue
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands; Institute of Forensic Medicine, Medical Center - University of Freiburg, Forensic Molecular Biology, Alberstrasse 9, 79104 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Timo Sänger
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Forensic Molecular Biology, Alberstrasse 9, 79104 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Huub C J Hoefsloot
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Sabine Lutz-Bonengel
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Forensic Molecular Biology, Alberstrasse 9, 79104 Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ate D Kloosterman
- Netherlands Forensic Institute, Biological Traces, Laan van Ypenburg 6, 2497GB Den Haag, The Netherlands; University of Amsterdam, Institute for Biodiversity and Dynamics, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Pernette J Verschure
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands.
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Pu J, Miura T, Kazama S, Konta Y, Azraini ND, Ito E, Ito H, Omura T, Watanabe T. Weekly variations in norovirus genogroup II genotypes in Japanese oysters. Int J Food Microbiol 2018; 284:48-55. [PMID: 29990639 DOI: 10.1016/j.ijfoodmicro.2018.06.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 06/01/2018] [Accepted: 06/29/2018] [Indexed: 11/20/2022]
Abstract
Increased levels of norovirus contamination in oysters were reportedly associated with a gastroenteritis epidemic occurring upstream of an oyster farming area. In this study, we monitored the norovirus concentration in oysters weekly between November 2014 and March 2015 and investigated the statistical relationship between norovirus genogroup II (GII) concentrations in oyster and sewage samples and the number of gastroenteritis cases in the area using cross-correlation analysis. A peak correlation coefficient (R = 0.76) at a time lag of +1 week was observed between the number of gastroenteritis cases and norovirus GII concentrations in oysters, indicating that oyster contamination is correlated with the number of gastroenteritis cases with a 1-week delay. Moreover, weekly variations in norovirus GII genotypes in oysters were evaluated using pyrosequencing. Only GII.3 was detected in November and December 2014, whereas GII.17 and GII.4 were present from January to March 2015. GII.17 Kawasaki 2014 strains were detected more frequently than GII.4 Sydney 2012 strains in oyster samples, as previously observed in stool and sewage samples collected during the same study period in Miyagi, Japan. Our observations indicate that there is a time lag between the circulation of norovirus genotypes in the human population and the detection of those genotypes in oysters.
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Konukiewitz B, Jesinghaus M, Steiger K, Schlitter AM, Kasajima A, Sipos B, Zamboni G, Weichert W, Pfarr N, Klöppel G. Pancreatic neuroendocrine carcinomas reveal a closer relationship to ductal adenocarcinomas than to neuroendocrine tumors G3. Hum Pathol 2018; 77:70-79. [PMID: 29596894 DOI: 10.1016/j.humpath.2018.03.018] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/06/2018] [Accepted: 03/06/2018] [Indexed: 12/29/2022]
Abstract
Pancreatic neuroendocrine carcinoma is a rare aggressive tumor commonly harboring TP53 and RB1 alterations and lacking neuroendocrine-related genetic changes such as mutations in MEN1 and ATRX/DAXX. Little is known about its genetic profile with regard to that of pancreatic ductal adenocarcinoma. We therefore conducted a detailed genetic study in 12 pancreatic neuroendocrine carcinomas of large cell (n = 9) and small cell type (n = 3) using massive parallel sequencing applying a 409-gene panel on an Ion Torrent system. The genetic data were compared with known data of pancreatic ductal adenocarcinoma and correlated with exocrine lineage marker expression. A similar analysis was performed in 11 pancreatic neuroendocrine tumors G3. Neuroendocrine carcinomas harbored 63 somatic mutations in 45 different genes, affecting most commonly TP53 (8/12 cases), KRAS (5/12 cases), and RB1 (loss of expression with or without deletion in 4/12 cases). Five carcinomas had both TP53 and KRAS mutations. Neuroendocrine tumors G3 only shared singular mutations in 5 different genes with neuroendocrine carcinomas, including TP53, CDKN2A, ARID1A, LRP1B, and APC, affecting 5 different cases. Most KRAS-positive neuroendocrine carcinomas also expressed MUC1 (4/5) and carcinoembryonic antigen (3/5) as markers of ductal differentiation. Our data indicate that almost half of the pancreatic neuroendocrine carcinomas are genetically and phenotypically related to pancreatic ductal adenocarcinoma, and might therefore respond to chemotherapies targeting the latter carcinomas.
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Affiliation(s)
- Björn Konukiewitz
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany.
| | - Moritz Jesinghaus
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany.
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany.
| | | | - Atsuko Kasajima
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany.
| | - Bence Sipos
- Institute of Pathology, University Hospital of Tuebingen, 72076 Tuebingen, Germany.
| | - Giuseppe Zamboni
- Institute of Pathology, Sacro Cuore Don Calabria Hospital, 37024 Negrar, Verona, Italy.
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany.
| | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany.
| | - Günter Klöppel
- Institute of Pathology, Technical University of Munich, 81675 Munich, Germany.
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Gonzalez-Martinez A, Muñoz-Palazon B, Maza-Márquez P, Rodriguez-Sanchez A, Gonzalez-Lopez J, Vahala R. Performance and microbial community structure of a polar Arctic Circle aerobic granular sludge system operating at low temperature. Bioresour Technol 2018; 256:22-29. [PMID: 29428610 DOI: 10.1016/j.biortech.2018.01.147] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 06/08/2023]
Abstract
The aim of this work was to study the performance and microbial community structure of a polar Arctic Circle aerobic granular sludge (AGS) system operating at low temperature. Thus, an AGS bioreactor was operated at 7, 5 and 3 °C of temperature using a cold-adapted sludge from Lapland. At 5 °C, it yielded acceptable conversion rates, in terms of nitrogen, phosphorous, and organic matter. However, under 3 °C a negligible nitrogen and phosphorous removal performance was observed. Below 5 °C, scanning electron microscopy studies showed a wispy, non-dense and irregular granular structure with a strong outgrowth of filamentous. Moreover, Illumina next-generation sequencing showed a heterogeneous microbial population where SM1K20 (Archaea), Trichosporon domesticum (Fungus), and Zooglea, Arcobacter and Acinetobacter (Bacteria) were the dominant phylotypes. Our study suggests that AGS technologies inoculated with North Pole sludge could be operated, in cold regions for a period longer than 3 months (winter season) under 5 °C of water temperature.
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Affiliation(s)
- Alejandro Gonzalez-Martinez
- Department of Built Environment, School of Engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076 Espoo, Finland.
| | - Barbara Muñoz-Palazon
- Institute of Water Research, University of Granada, Ramón y Cajal, 4, 18071 Granada, Spain
| | - Paula Maza-Márquez
- Institute of Water Research, University of Granada, Ramón y Cajal, 4, 18071 Granada, Spain
| | | | - Jesus Gonzalez-Lopez
- Institute of Water Research, University of Granada, Ramón y Cajal, 4, 18071 Granada, Spain
| | - Riku Vahala
- Department of Built Environment, School of Engineering, Aalto University, P.O. Box 15200, Aalto, FI-00076 Espoo, Finland
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Abstract
MicroRNAs are a class of small noncoding RNAs that function as regulators involving in many biological processes. The evaluation of miRNAs and their targets has been aided by miRNA expression profiling studies including multiplex PCR, microarrays, and recent next-generation sequencing tools. Next-generation sequencing has enabled us to profile thousands of genes in a single experiment and overcome the background signal and cross-hybridization issues of microarrays. Next-generation sequencing also allows for the simultaneous confirmation of known miRNAs and discovery of new miRNAs, and significantly reduces costs while providing billions of nucleotide information within a single experiment. Here we describe a detailed procedure of generation of miRNA library for next-generation sequencing to increase the efficiency of adapter ligation and finally construct a more specific cDNA library for sequencing and analyses for miRNA expression profiling.
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Affiliation(s)
- Poching Liu
- DNA Sequencing and Genomics Core-NHLBI, National Institute of Health, Bethesda, MD, USA.
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42
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Nakanishi H, Pereira V, Børsting C, Yamamoto T, Tvedebrink T, Hara M, Takada A, Saito K, Morling N. Analysis of mainland Japanese and Okinawan Japanese populations using the precision ID Ancestry Panel. Forensic Sci Int Genet 2017; 33:106-109. [PMID: 29223883 DOI: 10.1016/j.fsigen.2017.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/18/2017] [Accepted: 12/05/2017] [Indexed: 01/28/2023]
Abstract
We typed 165 AIMs in 49 mainland Japanese and 47 Okinawa Japanese using the Precision ID Ancestry Panel (Thermo Fisher Scientific). None of the 165 SNPs showed significant deviation from Hardy-Weinberg equilibrium in the mainland Japanese. One SNP (rs3943253) showed significant deviation from Hardy-Weinberg equilibrium in Okinawa Japanese. Fisher's exact tests showed that the genotype frequencies of 14 loci were significantly different (p<0.05) between the two populations before correction for multiple testing. After Bonferroni correction, only rs671 remained statistically significant (p<0.0003). This SNP is located in the ALDH2 gene. The mutant A allele is associated with increased side effects after alcohol intake. The frequency of the GG genotype (wild type) was higher in the Okinawa Japanese (78.7%) than in mainland Japanese (34.7%; Bonferroni corrected P<0.001). For 31 (63.3%) of the mainland Japanese and 42 (89.4%) of Okinawa Japanese, the highest population likelihood was obtained with the Japanese reference population. However, only in a few individuals, the likelihoods were significantly different from those calculated using reference data from neighboring populations. The likelihoods for mainland Japanese and Okinawa Japanese were not significantly different from each other for any of the investigated individuals. STRUCTURE and PCA analyses showed that mainland Japanese, Okinawa Japanese, and East Asians could not be differentiated with the Precision ID Ancestry Panel.
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Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, Japan; Department of Forensic Medicine, Saitama Medical University, Morohongo, Moroyama, Saitama, Japan
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Toshimichi Yamamoto
- Department of Legal Medicine and Bioethics, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | | | - Masaaki Hara
- Department of Forensic Medicine, Saitama Medical University, Morohongo, Moroyama, Saitama, Japan
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, Morohongo, Moroyama, Saitama, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, Japan; Department of Forensic Medicine, Saitama Medical University, Morohongo, Moroyama, Saitama, Japan
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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Naue J, Hoefsloot HCJ, Mook ORF, Rijlaarsdam-Hoekstra L, van der Zwalm MCH, Henneman P, Kloosterman AD, Verschure PJ. Chronological age prediction based on DNA methylation: Massive parallel sequencing and random forest regression. Forensic Sci Int Genet 2017; 31:19-28. [PMID: 28841467 DOI: 10.1016/j.fsigen.2017.07.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 07/26/2017] [Accepted: 07/30/2017] [Indexed: 01/24/2023]
Abstract
The use of DNA methylation (DNAm) to obtain additional information in forensic investigations showed to be a promising and increasing field of interest. Prediction of the chronological age based on age-dependent changes in the DNAm of specific CpG sites within the genome is one such potential application. Here we present an age-prediction tool for whole blood based on massive parallel sequencing (MPS) and a random forest machine learning algorithm. MPS allows accurate DNAm determination of pre-selected markers and neighboring CpG-sites to identify the best age-predictive markers for the age-prediction tool. 15 age-dependent markers of different loci were initially chosen based on publicly available 450K microarray data, and 13 finally selected for the age tool based on MPS (DDO, ELOVL2, F5, GRM2, HOXC4, KLF14, LDB2, MEIS1-AS3, NKIRAS2, RPA2, SAMD10, TRIM59, ZYG11A). Whole blood samples of 208 individuals were used for training of the algorithm and a further 104 individuals were used for model evaluation (age 18-69). In the case of KLF14, LDB2, SAMD10, and GRM2, neighboring CpG sites and not the initial 450K sites were chosen for the final model. Cross-validation of the training set leads to a mean absolute deviation (MAD) of 3.21 years and a root-mean square error (RMSE) of 3.97 years. Evaluation of model performance using the test set showed a comparable result (MAD 3.16 years, RMSE 3.93 years). A reduced model based on only the top 4 markers (ELOVL2, F5, KLF14, and TRIM59) resulted in a RMSE of 4.19 years and MAD of 3.24 years for the test set (cross validation training set: RMSE 4.63 years, MAD 3.64 years). The amplified region was additionally investigated for occurrence of SNPs in case of an aberrant DNAm result, which in some cases can be an indication for a deviation in DNAm. Our approach uncovered well-known DNAm age-dependent markers, as well as additional new age-dependent sites for improvement of the model, and allowed the creation of a reliable and accurate epigenetic tool for age-prediction without restriction to a linear change in DNAm with age.
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Affiliation(s)
- Jana Naue
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands.
| | - Huub C J Hoefsloot
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Olaf R F Mook
- Amsterdam Medical Center, Clinical Genetics, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Laura Rijlaarsdam-Hoekstra
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Marloes C H van der Zwalm
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Peter Henneman
- Amsterdam Medical Center, Clinical Genetics, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Ate D Kloosterman
- Netherlands Forensic Institute, Biological Traces, Laan van Ypenburg 6, 2497GB Den Haag, The Netherlands; University of Amsterdam, Institute for Biodiversity and Dynamics, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Pernette J Verschure
- University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands.
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Gago-Díaz M, Ramos-Luis E, Zoppis S, Zorio E, Molina P, Braza-Boïls A, Giner J, Sobrino B, Amigo J, Blanco-Verea A, Carracedo Á, Brion M. Postmortem genetic testing should be recommended in sudden cardiac death cases due to thoracic aortic dissection. Int J Legal Med 2017; 131:1211-1219. [PMID: 28391405 DOI: 10.1007/s00414-017-1583-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 03/27/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Acute thoracic aortic dissections and ruptures, the main life-threatening complications of the corresponding aneurysms, are an important cause of sudden cardiac death. Despite the usefulness of the molecular diagnosis of these conditions in the clinical setting, the corresponding forensic field remains largely unexplored. The main goal of this study was to explore and validate a new massive parallel sequencing candidate gene assay as a diagnostic tool for acute thoracic aortic dissection autopsy cases. MATERIALS AND METHODS Massive parallel sequencing of 22 thoracic aortic disease candidate genes performed in 17 cases of thoracic aortic dissection using AmpliSeq and Ion Proton technologies. Genetic variants were filtered by location, type, and frequency at the Exome Aggregation Consortium and an internal database and further classified based on the American College of Medical Genetics and Genomics (ACMG) recommendations published in 2015. All prioritized results were confirmed by traditional sequencing. RESULTS From the total of 10 potentially pathogenic genetic variants identified in 7 out of the 17 initial samples, 2 of them were further classified as pathogenic, 2 as likely pathogenic, 1 as possibly benign, and the remaining 5 as variants of uncertain significance, reaching a molecular autopsy yield of 23%, approximately. CONCLUSIONS This massive parallel sequencing candidate gene approach proved useful for the molecular autopsy of aortic dissection sudden cardiac death cases and should therefore be progressively incorporated into the forensic field, being especially beneficial for the anticipated diagnosis and risk stratification of any other family member at risk of developing the same condition.
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Affiliation(s)
- Marina Gago-Díaz
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Eva Ramos-Luis
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Silvia Zoppis
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain.,Laboratorio di Genetica Forense, Sezione di Medicina Legale, Dipartimento S.A.I.M.L.A.L., Università di Roma Sapienza, Rome, Italy
| | - Esther Zorio
- Servicio de Cardiología, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Pilar Molina
- Servicio de Patología, Instituto de Medicina Legal de Valencia, Valencia, Spain
| | | | - Juan Giner
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Beatriz Sobrino
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Jorge Amigo
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Alejandro Blanco-Verea
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
| | - María Brion
- Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain. .,Grupo de Medicina Xenómica, Instituto de Investigación Sanitaria de Santiago de Compostela, Universidade de Santiago de Compostela, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain. .,Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Laboratorio 1, Travesía de Choupana S/N, CP: 15706, Santiago de Compostela, Spain.
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Elsensohn MH, Leblay N, Dimassi S, Campan-Fournier A, Labalme A, Roucher-Boulez F, Sanlaville D, Lesca G, Bardel C, Roy P. Statistical method to compare massive parallel sequencing pipelines. BMC Bioinformatics 2017; 18:139. [PMID: 28249565 PMCID: PMC5333416 DOI: 10.1186/s12859-017-1552-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 02/16/2017] [Indexed: 02/01/2023] Open
Abstract
Background Today, sequencing is frequently carried out by Massive Parallel Sequencing (MPS) that cuts drastically sequencing time and expenses. Nevertheless, Sanger sequencing remains the main validation method to confirm the presence of variants. The analysis of MPS data involves the development of several bioinformatic tools, academic or commercial. We present here a statistical method to compare MPS pipelines and test it in a comparison between an academic (BWA-GATK) and a commercial pipeline (TMAP-NextGENe®), with and without reference to a gold standard (here, Sanger sequencing), on a panel of 41 genes in 43 epileptic patients. This method used the number of variants to fit log-linear models for pairwise agreements between pipelines. To assess the heterogeneity of the margins and the odds ratios of agreement, four log-linear models were used: a full model, a homogeneous-margin model, a model with single odds ratio for all patients, and a model with single intercept. Then a log-linear mixed model was fitted considering the biological variability as a random effect. Results Among the 390,339 base-pairs sequenced, TMAP-NextGENe® and BWA-GATK found, on average, 2253.49 and 1857.14 variants (single nucleotide variants and indels), respectively. Against the gold standard, the pipelines had similar sensitivities (63.47% vs. 63.42%) and close but significantly different specificities (99.57% vs. 99.65%; p < 0.001). Same-trend results were obtained when only single nucleotide variants were considered (99.98% specificity and 76.81% sensitivity for both pipelines). Conclusions The method allows thus pipeline comparison and selection. It is generalizable to all types of MPS data and all pipelines. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1552-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M H Elsensohn
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, 162 avenue Lacassagne, F-69003, Lyon, France. .,Université de Lyon, Lyon, France. .,Université Lyon 1, Villeurbanne, France. .,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France.
| | - N Leblay
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, 162 avenue Lacassagne, F-69003, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France
| | - S Dimassi
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - A Campan-Fournier
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - A Labalme
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - F Roucher-Boulez
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - D Sanlaville
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - G Lesca
- Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, CNRS UMR 5292, INSERM U1028, Lyon, France
| | - C Bardel
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, 162 avenue Lacassagne, F-69003, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France
| | - P Roy
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, 162 avenue Lacassagne, F-69003, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Villeurbanne, France.,CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Equipe Biostatistique Santé, Villeurbanne, France
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Abstract
Rare disorders constitute a large and heterogeneous group of diagnoses of which many cause chronic disabilities with significant impact on the lives of affected individuals and their families as well as on the health-care system. Each individual disorder is rare, but when considered as a group, rare disorders are common with a total prevalence of approximately 6-8%. The clinical presentation of these disorders includes a broad diversity of symptoms and signs, often involving the nervous system and resulting in symptoms such as intellectual disability, neuropsychiatric disorders, epilepsy and motor dysfunction. The methods for establishing an etiological diagnosis in patients with rare disorders have improved dramatically during recent years. With the introduction of genomic screening methods, it has been shown that the cause is genetic in the majority of the patients and many will receive an etiological diagnosis in a clinical setting. However, there are a lot of challenges in diagnosing these disorders and despite recent years' advances, a large number of patients with rare disorders still go without an etiological diagnosis. In this chapter we will review the etiology of rare disorders with focus on intellectual disability and what has been learned from massive parallel sequencing studies in deciphering the genetic basis. Furthermore, we will discuss challenges in the etiological diagnostics of these disorders including issues that regard interpretation of the numerous genetic variants detected by genomic screening methods and challenges in the translation of massive parallel sequencing technologies into clinical practice.
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47
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Hyppa RW, Fowler KR, Smith GR. Quantitative Genome-Wide Measurements of Meiotic DNA Double-Strand Breaks and Protein Binding in S. pombe. Methods Mol Biol 2017; 1471:25-49. [PMID: 28349389 PMCID: PMC5771505 DOI: 10.1007/978-1-4939-6340-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
The fission yeast Schizosaccharomyces pombe is especially well suited for studying meiosis in molecular detail. Experiments with S. pombe strains that undergo a nearly synchronous meiosis-at variable temperatures-have elucidated the mechanisms of meiotic progression and the proteins that are involved. For example, studies focused on the initiation of meiotic recombination by programmed DNA double-strand breaks (DSBs) have proven exceptionally informative. In meiosis, some regions of DNA have more frequent DSBs than the surrounding regions. These DSB hotspots can be visualized by Southern blot hybridization of restriction fragments ranging from kilobases (kb) to megabases (Mb) in size. More recently, the benefits of genome-wide analysis to map the distribution and frequency of meiotic DSBs have been attained, with resolution down to the nucleotide level. Infrequent, non-hotspot DSBs previously not detectable have been observed, creating a better understanding of how recombination is regulated. Additional genome-wide analyses have shown proteins that bind specifically to DSB hotspots, providing insight into how the DSB initiation complex functions. We describe here detailed methods for achieving these results.
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Affiliation(s)
- Randy W Hyppa
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kyle R Fowler
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
| | - Gerald R Smith
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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48
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Abstract
Major depressive disorder (MDD) is a multifactorial disease, weakly linked to multiple genetic risk factors. In contrast to that, environmental factors and "gene × environment" interaction between specific risk genes and environmental factors, such as severe or early stress exposure, have been strongly linked to MDD vulnerability. Stressors can act on the interface between an organism and the environment, the epigenome. The molecular foundation for the impact of stressors on the risk to develop MDD is based on the hormonal stress response itself: the glucocorticoid receptor (GR, encoded by NR3C1). NR3C1 can directly interact with the epigenome in the cell nucleus. Besides DNA methylation, histone modifications have been reported to be crucial targets for the interaction with the stress response system. Here, we review critical findings on the impact of the most relevant histone modifications, i.e. histone acetylation and methylation, in the context of MDD and related animal models. We discuss new treatment options which have been based on these findings, including histone deacetylase inhibitors (HDACis) and drugs targeting specific histone marks, closely linked to psychiatric disease. In this context we talk about contemporary and future approaches required to fully understand (1) the epigenetics of stress-related disease and (2) the mode of action of potential MDD drugs targeting histone modifications. This includes harnessing the unprecedented potentials of genome-wide analysis of the epigenome and transcriptome, in a cell type-specific manner, and the use of epigenome editing technologies to clearly link epigenetic marks on specific genomic loci to functional relevance.
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Affiliation(s)
- Jan M Deussing
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Kraepelinstr. 2, 80804, Munich, Bavaria, Germany
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Kraepelinstr. 2, 80804, Munich, Bavaria, Germany.
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49
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Spier I, Kerick M, Drichel D, Horpaopan S, Altmüller J, Laner A, Holzapfel S, Peters S, Adam R, Zhao B, Becker T, Lifton RP, Holinski-Feder E, Perner S, Thiele H, Nöthen MM, Hoffmann P, Timmermann B, Schweiger MR, Aretz S. Exome sequencing identifies potential novel candidate genes in patients with unexplained colorectal adenomatous polyposis. Fam Cancer 2016; 15:281-8. [PMID: 26780541 DOI: 10.1007/s10689-016-9870-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In up to 30% of patients with colorectal adenomatous polyposis, no germline mutation in the known genes APC, causing familial adenomatous polyposis, MUTYH, causing MUTYH-associated polyposis, and POLE or POLD1, causing Polymerase-Proofreading-associated polyposis can be identified, although a hereditary etiology is likely. To uncover new causative genes, exome sequencing was performed using DNA from leukocytes and a total of 12 colorectal adenomas from seven unrelated patients with unexplained sporadic adenomatous polyposis. For data analysis and variant filtering, an established bioinformatics pipeline including in-house tools was applied. Variants were filtered for rare truncating point mutations and copy-number variants assuming a dominant, recessive, or tumor suppressor model of inheritance. Subsequently, targeted sequence analysis of the most promising candidate genes was performed in a validation cohort of 191 unrelated patients. All relevant variants were validated by Sanger sequencing. The analysis of exome sequencing data resulted in the identification of rare loss-of-function germline mutations in three promising candidate genes (DSC2, PIEZO1, ZSWIM7). In the validation cohort, further variants predicted to be pathogenic were identified in DSC2 and PIEZO1. According to the somatic mutation spectra, the adenomas in this patient cohort follow the classical pathways of colorectal tumorigenesis. The present study identified three candidate genes which might represent rare causes for a predisposition to colorectal adenoma formation. Especially PIEZO1 (FAM38A) and ZSWIM7 (SWS1) warrant further exploration. To evaluate the clinical relevance of these genes, investigation of larger patient cohorts and functional studies are required.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany. .,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany.
| | - Martin Kerick
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Dmitriy Drichel
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Sukanya Horpaopan
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.,Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Andreas Laner
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medizinisch Genetisches Zentrum, Munich, Germany
| | - Stefanie Holzapfel
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Ronja Adam
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
| | - Bixiao Zhao
- Departments of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Tim Becker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Institute of Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
| | - Richard P Lifton
- Departments of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,Medizinisch Genetisches Zentrum, Munich, Germany
| | - Sven Perner
- Section for Prostate Cancer Research, Center for Integrated Oncology Cologne/Bonn, Institute of Pathology, University Hospital of Bonn, Bonn, Germany.,Pathology Network of the University Hospital of Luebeck and Leibniz Research Center Borstel, Borstel, Germany
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,Division of Medical Genetics, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Bernd Timmermann
- Next Generation Sequencing Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michal R Schweiger
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.,Center for Hereditary Tumor Syndromes, University of Bonn, Bonn, Germany
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50
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Mendoza-Parra MA, Saleem MAM, Blum M, Cholley PE, Gronemeyer H. NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets. Methods Mol Biol 2016; 1418:243-65. [PMID: 27008019 DOI: 10.1007/978-1-4939-3578-9_13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The combination of massive parallel sequencing with a variety of modern DNA/RNA enrichment technologies provides means for interrogating functional protein-genome interactions (ChIP-seq), genome-wide transcriptional activity (RNA-seq; GRO-seq), chromatin accessibility (DNase-seq, FAIRE-seq, MNase-seq), and more recently the three-dimensional organization of chromatin (Hi-C, ChIA-PET). In systems biology-based approaches several of these readouts are generally cumulated with the aim of describing living systems through a reconstitution of the genome-regulatory functions. However, an issue that is often underestimated is that conclusions drawn from such multidimensional analyses of NGS-derived datasets critically depend on the quality of the compared datasets. To address this problem, we have developed the NGS-QC Generator, a quality control system that infers quality descriptors for any kind of ChIP-sequencing and related datasets. In this chapter we provide a detailed protocol for (1) assessing quality descriptors with the NGS-QC Generator; (2) to interpret the generated reports; and (3) to explore the database of QC indicators (www.ngs-qc.org) for >21,000 publicly available datasets.
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Affiliation(s)
- Marco Antonio Mendoza-Parra
- Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France.
| | - Mohamed-Ashick M Saleem
- Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France
| | - Matthias Blum
- Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France
| | - Pierre-Etienne Cholley
- Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France
| | - Hinrich Gronemeyer
- Equipe Labellisée Ligue Contre le Cancer, Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/CNRS/INSERM/Université de Strasbourg, BP 10142, 67404, Illkirch Cedex, France
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